bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction of metallic cations with DNA VI. Specific binding of Mg++ and Mn++
Authors: Clement R. M. , Sturm J. , Daune M. P. 
Published: December 2004

AbstractThe binding of Mg2+ and Mn2+ by DNA by a divalent cation specific electrode and by ultracentrifugation. Both techniques give similar results for the stoichiometry of the reaction. An oscillating densiemete allowed us to detect small changes of volume accompanying the binding. The reaction was also followed by circular dichroism measurements. Interpretation of the results is only possible if one assumes an electrostate site‐binding of Mg2+ to phosphate group, and a chelation Mn2+ between the phosphate group and the N7 of the guanine. Physical modifications accompanying these two types of binding are discused and compared to the role of these cations in some biological systems involving DNA.
A comparison of the interactions of proflavine with DNA and with deoxyribonucleohistone using circular dichroism spectroscopy
Authors: Dalgleish D. G. , Dingsøyr E. , Peacocke A. R. 
Published: December 2004

AbstractComplexes of proflavine with DNA and deoxyribonucleohistone from calf thymus show different optical activity in the visible and the ultraviolet. Although the visible CD spectra of both complexes arise from interactions of dye molecules, the variation in the optical activity with the amount of dye bound suggests that a lesser conformational mobility exists in DNH. This is confirmed by the ultraviolet CD spectra of the complexes, and it is suggested that the conformation of DNA within nucleohistone is altered by separation of the base pairs by a greater extent than occurs in DNA in free solution. Even if the protein is unequally distributed along the DNA, the conformation of all of the DNA is altered by its incorporation into the nucleoprotein complex, since no evidence could be detected to show that DNA in a “free” conformation existed.
The electrostatic potential of a discretely charged cylinder in solution
Authors: Bailey James M. 
Published: December 2004

AbstractThe electrostatic potential of an infinitely long cylinder with a periodic, discrete charge density was calculated, assuming the cylinder was immersed in a simple 1 : 1 electrolyte solution. The charge density of the simple electrolyte was taken to be the linearized Debye‐Hückel charge density. It was also assumed that the discrete charge density, was within the cylinder (rather than on its surface), and that the interior of the cylinder had a unique dielectric constant Dh, which was treated as a parameter. Although this model (except for the Debye‐Hückel assumption) more realistically represents DNA than previous models, the calculated potential was found to be ambiguous, depending on the value chosen for the depth of the discrete charge below the cylinder surface. However it was also found that the dependence of the potential on the simple electrolyte concentration was well‐defined and was identical to that of a continuously charged cylinder. It was concluded that the continuously charged cylinder model adequately describes differential salt effects.
Observation of small conformational changes in the sperm‐whale myoglobin by the far‐infrared spectra
Authors: Chirgadze Yu. N. , Ovsepyan A. M. 
Published: December 2004

AbstractSmall conformational changes in a molecule of sperm‐whale myoglobin in its native solid state for different pH values at room temperature as well as during heat denaturation in alkali medium at different stages of unfolding of the globule were observed by using far‐infrared spectroscopy in the region from 30 to 600 cm−1. The changes appeared in the absorption bands near 420 and 470 cm−1 ascribed to the side‐chain vibrations of helical segments of the myoglobin molecule. For the first time the high structural sensitivity of the far‐infrared region of the skeletal vibrations has been confirmed experimentally and the applicability of this technique to globular proteins demonstrated.
Far‐infrared spectra of sequential polypeptides with α‐helical and polyglycine II structures
Authors: Itoh Koichi , Katabuchi Hiroaki 
Published: December 2004

AbstractThe sequential copolymers of glycine and L‐alanine, L‐valine and L‐alanine, L‐leucine and L‐alanine, and L‐phenylalanine and L‐alanine and those containing the L‐proline residues were synthesized. The infrared spectra in the region from 700 to 200 cm‐1 were measured for these polypeptides with the α‐helical conformation or the polyglycine II structure and compared with the spectra of the β‐form structures. The results showed that several infrared bands observed in the region from 600 to 200 cm‐1 clearly reflect not only the backbone conformations but also the local conformations of component amino acid residues of polypeptides with the α‐helical, β‐form and polyglycine II structures.
Kinetics of the acid hydrolysis of heparin from its Cu (II) complex and its relation to biological activity
Authors: Stivala Salvatore S. , Yadlowsky Slawko , Yuan Leon 
Published: December 2004

AbstractThe acid‐catalyzed hydrolysis of heparin from Cu(II) complex was studied as a function of time and temperature. Four independent calculations showed that the hydrolysis, during the 5‐hr period examined, obeys the first‐order kinetic law. Specific rate constants, calculated at 50°C, 57°C, 65°C, 71°C, and 80°C, were 3.3 × 10−5 sec−1, 6.5 × 10−5 sec−1, 10.4 × 10−5 sec−1, 15.1 × 10−5 sec−1, and 26.6 × 10−5 sec−1, respectively. Arrhenius plots of the data yielded 14.7 kcal as the energy of activation. An independent run of the self‐hydrolysis of heparin at 57°C also obeyed first‐order kinetics and its specific rate constant of 6.4 × 10−5 sec−1 is in excellent agreement with that of the hydrolysis of Cu(II)‐heparin at 57°C. The anticoagulant activity of heparin and of the Cu(II)‐heparin are not appreciably different. Further, the inactivation of heparin closely parallels Cu(II) release from the Cu(II) complex which in turn parallels desulfation.
Copper ion binding and heparin interactions of human fibrinogen
Authors: Lages Bruce , Stivala S. S. 
Published: December 2004

AbstractThe binding of copper ions to fibrinogen was studied by the equilibrium dialysis technique in neutral Tris buffer. The presence of copper causes precipitation of fibrinogen‐copper complexes, the amount of which varies with the copper ion concentration. Solutions of 96% clottable fibrinogen (whole fibrinogen) displayed a maximum binding capacity about four times greater than that of fibrinogen solutions from which the cold‐insoluble precipitate had been removed (cold‐soluble fibrinogen). Binding in both systems apparently involves two classes of sites in fibrinogen, and the class of lower affinity is associated with cooperative interactions with copper. The copper concentration at which this cooperative uptake occurs is identical to the concentration at which the amount of precipitated material increases sharply and also to the concentration at which a sharp decrease is observed in the sedimentation coefficient of soluble fibrinogen, suggesting some relationship between copper binding, solubility, and solution properties.The presence of heparin markedly affects the sedimentation coefficient of fibrinogen in the presence of copper ions, although showing a lesser effect in the absence of the metal. The sedimentation coefficient of fibrinogen is increased in the presence of heparin and copper ion, compared to the value of fibrinogen‐copper systems without heparin, and this effect is enhanced by changing the fibrinogen:heparin molar ratio to larger values. The precipitation of fibrinogen from solution, apparently without a coincident removal of heparin, also increases with increasing copper ion concentration and fibrinogen:heparin molar ratio. The possible significance of these effects in terms of heparin anti‐coagulant activity is discussed.
Rotational relaxation of macromolecules determined by dynamic light scattering. I. Tobacco mosaic virus
Authors: Schurr J. Michael , Schmitz Kenneth S. 
Published: December 2004

AbstractThe intensity autocorrelation function for the depolarized component of forward‐scattered light from a solution of large polymeric molecules is derived in terms of the correlation function for the amplitudes of the Y2,±1(θ,ϕ) fluctuations in the anglar distribution of segments in the solution without any assumptions regarding the statistical properties of the scatterad light field. Effects arising from the use of polychromatic incident light and from the mixing of the scattered and polychromatic incident light beams are examined in detail.Apparatus for observing the depolarized forward‐scattered light, digitizing and storing the fluctuating phototube current at rates from 10 to 540,000 times per second, and computing the correlation functions directly in the time‐domain is described herein. Correlation functions were obtained for 0.05 mg/ml solution of tobacco mosaic virus at pH 9.1 and also at pH 6. The degree of association of the virus appears to be independent of pH, and the monomer relaxation times (corrected to 25°C) extracted from the data by a least‐squares procedure lie in the range 0.44–0.49 msec, also independent of pH. The absence of faster component in the correlation function between 6 μsec and 0.5 msec is used in conjunction with thermal fluctuation theory to infer a lower limit for the effective Young's modulaus of the rod, E ≤ 2.5 × 107 dynes/cm2.
Dielectric study of the urea denaturation of delipidated and relipidated bovine serum albumin
Authors: Rosseneu‐Motreff M. Y. , Soetewey F. , Lamote R. , Peeters H. 
Published: December 2004

AbstractDielectric relaxation and viscosity measurements were performed on delipidated and relipidated samples of bovine serum albumin (BSA) at urea concentrations between O and 6M. By the combined interpretation of these two hydrodynamic methods the characterization of conformational changes of the molecule during urea denaturation is possible.The denaturation of delipidated BSA results from two mechanisms. The first one is a slow, time‐dependent elongation of the molecule; the second one is a rapid swelling which becomes most pronounced at urea concentrations higher than 4M. For relipidated albumin, the slow elongation mechanism occurs but the presence of fatty acids protects the protein aganist molecular swelling. In both cases these conformational changes are accompanied by an increased disymmetry of charge repartition and a concomitant increase of the dipole moment.From these results it follows that lipidated albumin (as occurs under physiological conditions) is less sensitive to denaturation than delipidated albumin.
Non‐bonded interatomic potential functions and crystal structure. Correction of the functions for use with macromolecules and application to polypeptide helixes
Authors: Nelson Donald J. , Hermans Jan 
Published: December 2004

AbstractOn the basis of a set of nonbonded interatomic potential functions derived earlier from heats of sublimation and experimental crystal structures, we derive a second, less repulsive, set which is to be used in the absence of the expansion caused by thermal motion and in particular in macromolecular systems where thermal motion is much reduced compared with crystals of small molecules. Working with a pair of octane molecules, we calculate the intermolecular potential (U) in the presence of thermal motion from potentials U° (in the absence of thermal motion), by letting a system of pairs of molecules assume a Boltzmann distribution over the intermolecular distance, in the presence of a force of varied magnitude applied to obtain different equilibrium distances. The potential U° is adjusted until the calculated and the empirical potentials U agree. Finally, best interatomic Lennard‐Jones potentials which reproduce the function U° are calculated. The resulting functions are tested by calculating the crystal structure of benzene and comparing it with experimental data at low temperature, by energy minimization of the crystal structure of polyethylene and of the β‐structure of poly‐L‐alanine, and by comparing the energy of the α‐helix and the β‐structure of poly‐L‐alanine. In all cases, the corrected functions give more satisfactory results than the uncorrected set.
The electrical properties and stability of DNA to UV radiation and aromatic hydrocarbons
Authors: Snart R. S. 
Published: December 2004

AbstractStudies of the d. c. conductive behavior of solid gels of DNA under high vacuum have shown that a reproducible energy gap of 2.4 eV and a photoelectric effect may be obtained following extensive evacuation procedures. Admission of air for short periods has a reversible effect on this photoelectirc effect and semiconductive behavior. After prolonged illumination in air the sample becomes permanently affected and will not reproduce the photoelectric effect or give rise to a semiconduction energy gap of 2.4 eV but give rise to a permanently lower energy gap of 1.6 eV. The effect of ultraviolet irradiation on the thermal denaturation of DNA in the presence of six aromatic hydrocarbons has been examined in order to determine the extent to which the presence of the hydrocarbon protects the DNA against ultraviolet damage.
Translational and rotational diffusion of tobacco mosaic virus from polarized and depolarized light scattering
Authors: King T. A. , Knox A. , McAdam J. D. G. 
Published: December 2004

AbstractThe translational and rotational dynamics of tobacco mosaic virus in sodium phosphate buffer (pH =7.5) solutions has been investigated by polarized and depolarized light scattering Rayleigh linewidth studies. For concentrations ranging from 1.75 × 10−4 g ml−1 to 0.25 × 10−4 g ml−1 the translational diffusion coefficient (DT) has been found to be slightly concentration dependent and extrapolation to zero concentration gives D020°C = 0.34 ± 0.01 × 10−7 cm2S−1. A full analysis of the polarized spectra obtained at high and low scattering angles and the depolarized spectra at near zero scattering angles has enabled these techniques to be compared and the rotational diffusion constant DR to be determined. At a solution concentration of 1.75 × 10−4 g ml−1 a mean value is found to be DR20°C = 350 ± 30s−1. These values of DT and DR are in approximate agreement with calculations based on models of the tobacco mosaic virus molecule as a cylindrical rod.
Oscillator strengthes of the 1La and 1Lb absorption bands of tryptophan and several other indoles
Authors: Strickland E. Hardin , Billups Carolyn 
Published: December 2004

AbstractThe intensities of the indolyl 1La and 1Lb absorption bands were investigated by using 5‐methoxyindole as a model compound. With 5‐methoxyindole dissolved in weakly interacting solvents, almost the entire 1Lb electronic transition occurs at longer wavelengths than the 1La transition. The resolved spectrum of 5‐methoxyindole permitted estimation of its oscillator strengths and also those of other indoles dissolved in cyclohexane: indole, 0.129 (1La), 0.019 (1Lb); 5‐methylindole, 0.129 (1La), 0.027 (1Lb); 5‐methoxyindole, 0.138 (1La), 0.045 (1Lb); 3‐methylindole and N‐stearyl‐L‐tryptophan n‐hexyl ester, 0.127 (1La), 0.027 (1Lb). Hydrogen bonding to 1‐methyl‐2‐pyrrolidinone does not measurably affect the total near‐ultraviolet oscillator strength of indoles (less than 5% change). In water and ethanol, the oscillator strength of 3‐methylindole and tryptophan is 15–20% less than that of 3‐methylindole dissolved in cyclohexane. The spectra of the N‐stearyl n‐hexyl esters of tryptophan and 1‐methyltryptophan dissolved in methylcyclohexane can be generated by using 1La and 1Lb bands having shapes similar to those observed for 5‐methoxyindole, if the 1La and 1Lb bands are shifted so that their O‐O bands overlap (289.5 nm for tryptophan and 299.5 nm for 1‐methyltryptophan).
Cooperative binding of oxygen to hemoglobin: Analysis of accurate equilibrium binding data
Authors: Deal Walter J. 
Published: December 2004

AbstractAccurate equilibrium binding data for the oxygenation of hemoglobin are used (a) to show that various models for cooperativity are inconsistent with the best available experimental data, (b) to determine the equilibrium constants for binding of 2,3‐diphosphoglycerate to hemoglobin molecules in intermediate stages of oxygenation, and (c) to deduce a mechanism for allosteric effects in hemoglobin which is consistent with the best available experimental data. The total free energy of cooperativity is defined and discussed.
Laser Raman studies of conformational variations of poly‐L‐lysine
Authors: Yu Tain‐Jen , Lippert Joseph L. , Peticolas Warner L. 
Published: December 2004

AbstractThe frequencies and intensities of the laser Raman spectra of poly‐L‐lysine (PLL) have been observed in the following studies: (1) the thermally induced α‐to‐β transition which occurs with increasing temperature at high pH; (2) the ionized form to α transition at 10°C by increasing pH; and (3) the ionized form to α transition by ionic strength at low pH.The frequency‐dependent bands which have been observed are the amide I (in H2O), amide I′ (in D2O), amide III, and C–C stretch. It has been found possible to assign an unique set of frequencies and intensities to each conformation of PLL of α, β, and ionized form. In this way the nature of the conformations intermediate in the transitions can be determined. The frequencies of the amide III and amide III′ are very weak in the α‐helix and somewhat higher than usual in the β form. Hence it appears the amide III and amide III′ bands may differ from one type of polypeptide to another with the same backbone conformation.
Low‐frequency vibrational spectra of some homopolypeptides in the solid state
Authors: Fanconi Bruno 
Published: December 2004

AbstractLow‐frequency Raman and far‐infrared spectra of polyglycine, poly‐L‐alanine, and poly‐L‐valine have been measured. The Raman spectra exhibit an intense band near 100 cm−1 for these homopolypeptides. Lattice calculations of the polyglycines are used to assign the intense Raman band to a rotary lattice mode. For homopolypeptides in the β conformation, an infrared band is observed whose frequency varies inversely with the square root of the mass of the peptide repeating unit. This infrared band is assigned to the hydrogen bond stretching lattice vibration.
Study by circular dichroism and optical rotatory dispersion of polypeptides with aromatic side‐chain chromophores
Authors: Barny Pierre Le , Loucheux‐Lefebvre Marie H. 
Published: December 2004

AbstractPoly(ortho‐, meta‐, and para‐γ‐nitrobenzyl‐L‐glutamates) were studied by circular dichroism (CD) and optical rotatory dispersion (ORD) in two helicogenic solvents, hexafluoroisopropanol (HFIP) and dichloroethane (EDC), and two non‐helicogenic solvents, dichloracetic acid (DCA) and trifluoroacetic acid (TFA). The corresponding glutamates were also studied in DCA and TFA. The symmetric nitrobenzylic chromophore is optically active when the polymers are in solution in DCA and TFA. The corresponding glutamates are also optically active under the same conditions. Thus, it was not possible to explain the origin of the optical activity of the side‐chain chromophore when the polymer is in solution in a helicogenic solvent. Nevertheless, from a side‐chain dichroic band, a helix–coil transition curve was determined and the stability of each poly(γ‐nitrobenzyl‐L‐glutamate) given; this stability depends on the position of the nitro substituent on the aromatic ring.
Calculated minimum energy. Conformations of nonactin
Authors: Lee Yan N. , Hamori Eugene 
Published: December 2004

AbstractNonactin is a cyclic actinomycete metabolite which has been implicated as an ion carrier in the passive transport of potassium across certain biological membranes. In order to discover the conformations of the molecule which are involved in its biochemical function, computer calculations were initiated to derive the energetically favored conformations of the nonactin ring. By assuming that all the relevant three‐dimensional conformations of nonactin have the same symmetry property as that suggested by the chemical structure of the molecule (S4) it was possible to generate a representative sample of all sterically allowed conformations of nonactin. The energies of these conformations were calculated by taking into account the nonbonded interactions among the 116 atoms of the molecule and the torsional potential energy of the 20 rotatable backbone bonds of the ring. The initial results reported in this paper indicate that even in the absence of potassium ion the nonactin ring folds into the same compact tennis‐ball seam‐like conformation that was found by an X‐ray crystallographic investigation of the nonactin/KNCS complex.
Interactions between mucopolysaccharides and cationic polypeptides in aqueous solution: Hyaluronic acid, heparitin sulfate, and keratan sulfate
Authors: Gelman R. A. , Blackwell J. 
Published: December 2004

AbstractCircular dichroism spectroscopy has been used to study the interactions of hyaluronic acid, heparitin sulfate, and keratan sulfate with cationic polypeptides. The results indicate that the presence of these mucopolysaccharides has an effect in the conformation of poly(L‐lysine) and poly(L‐arginine), such that the former adopts the “random” form and the latter takes up the α‐helical conformation, rather than the “charged coil” form expected at neutral pH. The relative strengths of the interactions can be judged from the melting temperatures above which they are disrupted. Both the stoichiometry and the strength of the interactions depend on the position, number, and type of anionic groups attached to the polysaccharide backbone. Such considerations place the six common mucopolysaccharides in order of increasing strength of interaction: hyaluronic acid < chondroitin 4‐sulfate < heparitin sulfate < chondroitin 6‐sulfate < keratan sulfate ⩽ dermatan sulfate. These differences should be paralleled by differences in the interaction of the mucopolysaccharides with collagen and fibrous proteins.
Circular dichroism of films of polynucleotides
Authors: Brunner Wendel C. , Maestre Marcos F. 
Published: December 2004

AbstractThe CD spectra of films of the lithium salt of E. coli and calf thymus DNA, and alternating d‐AT : AT were measured as a function of relative humidity. Films of the ammonium acetate salt of DNA were also measured. The ammonium films yield the previously reported A‐form CD spectra. A possible explanation for the small magnitude of the 260‐nm band of the A‐form film spectra compared to double‐stranded RNA spectra is that the film DNA is in a different conformation than RNA within the A family of conformations.At relative humidities of 92% or lower, a negative nonconservative CD spectrum with negative minima near 270 and 210 nm is observed with the lithium films. The magnitude of the minima varies from film to film. In films of DNA the magnitude ranges from a delta epsilon of −5 to −35; d‐AT : AT films show magnitudes to −300. CD spectra of this type are designated Ψ spectra. Similar spectra have been reported from reconstituted complexes of DNA and polylysine or f‐1 histone. If the origins of the film and protein–DNA complex spectra are similar, the complex spectra are not the result of specific secondary structural changes induced in the DNA by the protein fraction. Theoretical analysis suggests that Ψ spectra are not the result of changes in the secondary or tertiary structure of DNA. Instead, the previously proposed explanation based on liquid crystals is favored. The DNA could form asymmetric structures with long‐range periodicity. It is likely that the observed CD spectra of f‐1 complexes are artifacts of DNA aggregation. The possibility that some other previously published spectra of protein–DNA complexes also reflect artifacts is suggested.