bluuebunny/crossref_metadata_2025_split huggingface dataset:
An absolute method for the determination of the persistence length of native DNA from electron micrographs
Authors: Frontali C. , Dore E. , Ferrauto A. , Gratton E. , Bettini A. , Pozzan M. R. , Valdevit E. 
Published: December 2004

AbstractInformation on spatial correlation in the tangent direction along electron microscope images of filamentous molecule is shown to be obtainable by the analysis of statistical fluctuations in curvature, yielding an absolute measure of the persistence parameter amicro. The relationship of amicro, a local, microscopic parameter, to the persistence length introduced by Kratky and Porod is discussed. The hypotheses underlying the assumed theoretical model concern (1) the shape of the angle distribution, assumed to be Gaussian; (2) the passage from a three‐ to a two‐dimensional situation, which is supposed to occur by deformation of the flexible chain in a manner that preserves the memory of the spatial correlation in orientation (except for the blocking of one degree of freedom); and (3) the adsorption conditions, which should meet the equilibrium requirement as closely as possible. The analytical method has been checked on computer simulated “Gaussian” molecules: the study of the simulated sample was essential in solving the problems connected with minimum statistics requirements and the effect of the reading error. Experimental images obtained for T2 DNA fragments at different ionic strengths by Kleinschmidt's adsorption technique have been analyzed by means of an automatic flying spot digitizer, the “Precision Encoder and Pattern Recognition.” The results show that adsorbed molecules do in fact “remember” the rigidity they possessed in solution and that the Gaussian hypothesis is well verified. Consequently, the slopes of log cosθ(l) or θ2(l) may be used indifferently in the estimate of amicro. The dependence of this parameter on ionic strength in the range explored shows the expected behavior.
Polyelectrolyte behavior of carrageenans in aqueous solutions
Authors: Rinaudo M. , Karimian A. , Milas M. 
Published: December 2004

AbstractOsmotic coefficients of sodium, potassium, and calcium counterions have been determined in aqueous solutions on kappa‐, iota‐, and lambda‐carrageenans at 25°C. The experimental results are correlated with the calculated ones from the limiting law of Manning. An orderd secondary structure exists in kappa‐ and iota‐carrageenans. Its stability is discussed as a function of temperature, ionic strength, and the nature of the counterions.
Effect of Mg++ and polyamines on proflavine binding to T2 DNA
Authors: Riemer Steven C. , Bloomfield Victor A. 
Published: December 2004

AbstractProflavine binding may be used as a probe of the environment and interactions of DNA. In this paper we report the effects of the divalent cations Mg++ and putrescine and the trivalent cation spermidine on the proflavine–Na DNA binding equilibrium. Difference spectroscopy at 430 nm was used to determine apparent proflavine–DNA binding constants K at several concentrations of each cation for temperatures between 15 and 43°C, and at a constant total ionic strength of 0.1M. Mg++, putrescine, and spermidine all have greater effects on K than expected on the basis of ionic strength alone in the order spermidine > Mg++ ≳ putrescine. van't Hoff analysis of K(T) enabled calculation of ΔH° and ΔS°, which are affected differently by each cation. These differences are discussed qualitatively in terms of such concepts as release of condensed counterions, localized or unlocalized condensation, hydration, and restriction of molecular and internal rotation.
Hydrodynamic properties of proteoglycan subunit from bovine nasal cartilage. Self‐association behaviour and interaction with hyaluronate studied by laser light scattering
Authors: Reihanian H. , Jamieson A. M. , Tang L. H. , Rosenberg L. 
Published: December 2004

AbstractMeasurements of translational diffusion coefficients by quasielastic laser light scattering, sedimentation coefficients, and intrinsic viscosities at zero shear of proteoglycan subunit fraction A1‐D1‐D1 isolated from bovine nasal septa are reported. Molecular weights and hydrodynamic dimensions are compared with those expected on the basis of structural models previously proposed. Comparison of the concentration dependence of the diffusion coefficient in the presence of NaCl and GdnHCl leads to the conclusion that significant self‐association behaviour of subunit occurs in the absence of GdnHCl. In the absence of added salt, anomalous nonlinear concentration dependence of Dt estimated from wide‐angle light‐scattering experiments is observed. In addition, Dt apparently becomes angle dependent. These results are interpreted in terms of the perturbation of normal translational diffusion of the monomer by strong repulsive intermolecular interactions due to the combined effects of long‐range electrostatic forces and macromolecular congestion at higher concentrations. By carrying out experiments at small scattering angles, it is possible to determine D for proteoglycan subunit in the absence of supporting electrolyte. Titration of a dilute solution of subunit with hyaluronic acid results in a sigmoidal behaviour of the Stokes radius, indicating the formation of complexes of higher molecular weight results from the noncovalent association of proteoglycan subunits with hyaluronate. Observation of Dt appears to provide a useful method for studying the proteoglycan subunit–hyaluronate interactions.
Effect of temperature on the limiting viscosity number of hyaluronic acid and chondroitin 4‐sulfate
Authors: Cleland Robert L. 
Published: December 2004

AbstractThe decrease in the limiting viscosity number [η] with temperature T for hyaluronic acid in nonalkaline solution and chondroitin 4‐sulfate in neutral and alkaline solutions may be expressed in terms of the temperature coefficient of the Kratky‐Porod persistence length a: d ln a/dT = −0.0040 (±0.0005). The result, while numerically somewhat smaller, resembles qualitatively that of cellulose derivatives. As in the latter case, standard conformational calculations underestimate the coefficient, which may be due to neglect of random occurrence of local conformational features of higher energy. In alkaline solution, large decreases in [η] of hyaluronic acid are accompanied by a positive temperature coefficient of [η]. This temperature effect is interpreted as an endothermal shift from the alkaline, low [η] form of the polymer to the neutral, high [η] form with increasing temperature.
Effect of some monohydric alcohols on the functional stability of bovine liver β‐galactosidase
Authors: Cordone Lorenzo , Izzo Vincenzo , Sgroi Giuseppe , Fornili Sandro L. 
Published: December 2004

AbstractWe report on experiments showing that the presence of some monohydric alcohols in the solution medium perturbs the kinetics of bovine liver β‐galactosidase. The effect increases with increasing alcohol concentration and alkyl group size. To explain this effect we suggest a model that considers the existence of functional and nonfunctional enzyme conformations in thermodynamical equilibrium. This equilibrium is dependent both on alcohol concentration and on alkyl group size.
Raman spectroscopic study of 2H‐ and 15N‐ substituted guanosines: Monomers, gels, and polymers
Authors: Delabar Jean‐Maurice , Guschlbauer Wilhelm 
Published: December 2004

Abstract15N‐labeled guanosines were synthesized and studied by Raman spectroscopy. The isotopic substitution was either on nitrogens 1, 2, and 3 or on nitrogens 7 and 9. These substituted guanosines and their partially or totally deuterated derivatives were compared under a variety of experimental conditions: in aqueous solution in the presence of 0.1M KCl at pH 7 at 60 and 10°C, i.e., in solution and in gel form. The sensitivity to nitrogen isotopic substitution of some of the “hypochromic” bands was defined. These spectra were also compared with those in acidic and basic solution. The body of these data was compared with the results on poly(guanylic acid) and on guanine‐containing polynucleotides and nucleic acids.
Intermolecular association and molecular weight of aggregates of a monodisperse homohexapeptide, Nps‐[Glu(OBzl)]6‐NHEt, in solution
Authors: Ikeda Shoichi , Okahashi Kenji 
Published: December 2004

AbstractLight scattering from the solutions of Nps‐[Glu(OBzl)]6‐NHEt in dioxane or ethylene dichloride has been measured at different concentrations, and a critical concentration of intermolecular association is found to exist, which is equal to the critical concentration of β‐form formation. The Debye plot of light scattering leads to the molecular weight of aggregates at the critical concentration, which corresponds to an aggregation number 15 in dioxane and 53 in ethylene dichloride. In the latter solvent the aggregates further associate into a larger aggregate consisting of 330 molecules when the concentration is increased beyond the critical concentration. The content of β‐form, which is a measure of number of hydrogen bonds, is derived from the ir data previously obtained. The results on the modes of intermolecular association and hydrogen bonding lead to possible structures of aggregates formed by both hydrogen bonds and other nonbonding side‐chain interactions.
The crystal and molecular structure of cyclo‐[‐(D‐Val‐Hyi‐Val‐D‐Hyi)3‐] (meso‐valinomycin, C60H102N6O18)
Authors: Pletnev V. Z. , Galitskii N. M. , Ivanov V. T. , Ovchinnikov Yu. A. 
Published: December 2004

AbstractThe crystal structure of the valinomycin analog, cyclo‐[(‐D‐Val‐Hyi‐Val‐D‐Hyi‐)3‐] (meso‐valinomycin, C60H102N6O18) has been determined by direct x‐ray diffraction procedures. The crystals are triclinic, space group P1, number of molecules per unit cell Z = 1, and cell parameters a = 11.831, b = 13.815, c = 14.889 Å, α = 109.54°, β = 116.10°, γ = 98.89°. The atomic coordinates for the C,N,O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation to R = 0.07.The structure is centrosymmetric and has a threefold axis of pseudosymmetry. The depsipeptide chain is in the form of a bracelet stabilized by six identical intramolecular 4 → 1 hydrogen bonds between the amide CO and NH groups. The ester carbonyls are oriented towards the symmetry axis, their O atoms forming an ellipsoidal molecular cavity. The isopropyl side chains are located on the molecular periphery. The structure found differs considerably from the conformation of the crystalline naturally occurring antibiotic, valinomycin, but completely resembles that of valinomycin and meso‐valinomycin in nonpolar solvents. In the crystal, meso‐valinomycin molecules form stacks. The molecular cavities situated in the stacks one above the other along the pseudo‐C3 axis form a continuous channel, the internal surface of which is lined by O atoms. The possible conformations of depsipeptides of the valinomycin series and their mode of action in membranes are discussed in the light of the data obtained.
Effect of salt on the stability of the pH 4.2 rA8 double helix in a series of organic/aqueous mixed solvents: A test of oligoelectrolyte theory
Authors: Breslauer Kenneth J. , Bodnar Catherine M. 
Published: December 2004

AbstractTemperature‐dependent uv absorption spectroscopy has been used to investigate the salt dependence of the order–disorder transition for the pH 4.2 rA8 double helix in 100% aqueous buffer and in a series of organic/aqueous mixed solvents. Melting temperature, Tm, data were obtained for the transitions in the different solvents by analysis of the uv melting curves. For the pure aqueous buffer solvent, the melting temperature was found to exhibit a reduced salt dependence (∂tm/∂ log Na+) when compared to the corresponding polymer. This reduction is explained in terms of end effects and is shown to be consistent with the theoretical treatments of oligoelectrolyte transitions developed by Record and Lohman [Biopolymers, 17, 159–166 (1978)]. In the mixed solvents, the salt dependence of the melting temperature (∂tm/∂ log Na+) is shown to exhibit a linear dependence on the bulk dielectric constant of the medium for all of the hydroxyl‐containing solvents studied. Significantly, N,N‐dimethylformamide demonstrated different behavior.
Study by circular dichroism of soluble fragments of elastin from porcine and normal and pathological human aortas
Authors: Davril Monique , Han Kia‐Ki , Loucheux‐Lefebvre Marie‐H. 
Published: December 2004

AbstractA CD study was carried out on elastin peptide samples obtained from porcine and normal and pathological human aortas. Different solubilization procedures were used: (1) an ethanolic‐KOH hydrolysis to obtain porcine κ‐elastins; (2) oxalic acid hydrolysis to obtain porcine α‐ and β‐elastins; and (3) enzymatic digestions and a partial acid hydrolysis to obtain porcine and human crosslinked peptides. The comparison of the results obtained from the dichroic study of porcine and normal human aorta peptides does not reveal any differences. On the contrary, the dichroic spectra obtained for the human pathological aorta peptides at different stages of atheromateous lesions exhibit some differences which are attributed to some variations of the conformation around the bridging zones.
Nuclear magnetic resonance investigation of lysine–oligopeptides and a complex with d(pA)3pGpC(pT)3
Authors: Davanloo Pari , Crothers Donald M. 
Published: December 2004

AbstractWe report proton magnetic resonance studies of a series of lysine oligopeptides in H2O solution. At pH 5 the protonated ε‐amino groups are seen as broad resonances; the peptide NH proton resonances are split by spin–spin coupling with the Cα‐H proton, and appear at positions which depend on position in the chain and on chain length. Assignments were made by the europium shift method, and we observed the expected effect of catalysis by the terminal —NH3+ of exchange of the adjacent peptide NH. Coupling constants and the temperature coefficient of chemical shift values were consistent with a non‐hydrogen‐bonded structure for the oligolysines. The rate and mechanism of NH hydrogen exchange were investigated by line‐broadening measurements of the peptide protons as a function of pH. Exchange was found to be OH− catalyzed, with large differences in the rate depending on position in the chain. Preliminary studies of the complex between double‐helical d(pA)3pGpC(pT)3 and tetra(L‐lysine) were performed using 1H‐ and 31P‐nmr techniques. Pmr spectra of the complex at pH values ranging from 3.98 to 8.15 showed very complicated patterns. Downfield shifts and reduction in exchange rates were observed for several tetra(L‐lysine) protons. 31P‐nmr spectra of the complex reveal an upfield shift of 1 ppm for 3′‐5′ phosphate diester resonances on complexation. 31P T1 relaxation times change little on complex formation at low temperature but are altered at higher temperature.
Effect of Centrifuge Speed on the Sedimentation of High‐Molecular‐Weight Bacteriophage G DNA
Authors: Krasin Frank 
Published: December 2004

AbstractLarge molecular weight bacteriophage G DNA, about five times larger than T2 DNA, was used to test Zimm's theory [(1974) Biophys. Chem. 1, 279–291] for the effect of rotor speed on the sedimentation of large linear monodisperse DNA. Sedimentation profiles from neutral sucrose gradinets at low and high rotor speeds show G DNA sedimenting from 1.8 to 0.7 times as fast as T2 DNA. Experimental measurements indicate that the sedimentation coefficient of G DNA decreases with increasing rotor speed about as fast as predicted by theory.
Incorporation of lone pairs into the electrostatic term in the empirical intra‐ and intermolecular energy calculations
Authors: Tvaroška Igor , Bleha Tomáš 
Published: December 2004

AbstractThe method hitherto used for estimating the electrostatic term in empirical intramolecular calculations of stable conformations of biologically important molecules and macromolecules and intermolecular calculations of molecular associations or packing energy in molecular crystals had been analyzed. It has been shown that the contribution of atomic hybridization moments is omitted in the calculation of electrostatic interactions from net atomic charges localized on nuclei which have been determined by standard quantum‐chemical methods. This contribution plays an important part in determining electrostatic interactions, mainly in molecules containing atoms with lone pairs. Simultaneously, a modified method for calculating the electrostatic term comprising the interaction of the lone pairs, which are represented by atomic hybridization moments, has been proposed. The relationship between the atomic hybridization moment and the bond angle has been expressed for some typical configurations occurring in biologically important molecules. Finally, this new approach is illustrated by results of the conformational analysis of some model compounds for biomolecules and compared with the approach used so far for the estimation of the electrostatic interaction in empirical methods of calculation of the intra‐ and intermolecular energy.
Composite predictions of secondary structures of lac repressor
Authors: Bourgeois Suzanne , Jernigan Robert L. , Szu Shousun C. , Kabat Elvin A. , Wu Tai Te 
Published: December 2004

AbstractThe secondary structure of the lac repressor protein proposed by Chou et al. has been modified to include the recent revisions in sequence. In addition to the Chou and Fasman method, five other methods were used; they include those of (1) Lim, (2) Ptitsyn and Finkelstein, (3) Burgess et al., (4) Bunting et al., and (5) Wu and Kabat. Any two individual methods gave results differing sharply from one another. Three or more methods were in agreement for 91, 39, and 126 residues in helix, in β, and in combined coil plus turn conformations, respectively; there were such agreements for a total of 256 of the 360 residues. Agreements in the amino‐terminal third of the molecule were found for 68% of the residues, whereas in the remainder of the molecule only 53% of the residues showed such agreements. Only two helix‐breaking and two β‐breaking tripeptides were inconsistent with the composite predictions by three or more methods. The large number of disagreements among the results for different methods indicates that only very limited information is provided by each method and that the basis on which they operate is not clear. There is no a priori reason for a composite prediction to be more reliable than any individual prediction, and such a procedure does not permit the determination of an unambiguous secondary structure. Since these methods were applied to lac repressor before any three‐dimensional crystallographic structure was known, the methods may ultimately be evaluated should such a structure become available.
Statistical‐mechanical treatment of violations of the double helix in supercoiled DNA
Authors: Anshelevich V. V. , Vologodskii A. V. , Lukashin A. V. , Frank‐Kamenetskii M. D. 
Published: December 2004

AbstractWe consider the problem of making allowance for superhelicity in the statistical‐mechanical calculations of fluctuational violations of the DNA double helix. A simple model is discussed, making it possible in the calculations to use an approach based on the theory of helix–coil transition in DNA. The proposed algorithms allow calculating the effect of superhelicity on the base‐pair fluctuational opening for any given sequence of nucleotides. An algorithm is also proposed allowing for the hairpin and cruciform structures in the palindromic regions of a sequence, as well as the open and helical states. The theory is used to calculate the melting curve for superhelical DNA at temperatures well below the melting point of the linear or nicked forms. The maps of opening probability are calculated for SV40 and ϕX174 DNA using their recently published complete nucleotide sequences. The data explain well the experimental results of probing the secondary structure of these DNA by single strand‐specific endonucleases.
Transient electric birefringence of T7 viral DNA
Authors: Rau Donald C. , Bloomfield Victor A. 
Published: December 2004

AbstractThe electric birefringence properties of intact bacteriophage T7 DNA are investigated as a function of field strength and ionic environment. At low field strengths, E < 40 V/cm, Kerr behavior is observed. The birefringence decay kinetics are consistent with a Gaussian chain viscoelastic treatment for an induced dipole model of orientation. The observed relaxation time for the longest mode is 37 msec, in 0.5 mM Na+ at 15°C, and is in agreement with flow experiments. In order to account for the observed differences in rise and decay kinetics, a field‐induced, anharmonic restoring force is postulated. The magnitude of the apparent induced dipole moment is found to be inversely proportional to the Debye‐Hückel shielding parameter κ for a series of Na+ concentrations. The magnitude of the induced dipole moment is found to be very sensitive to the addition of Mg2+. When analyzed in terms of the counterion condensation theory of Manning, it appears that the induced dipole moment is proportional to the square of the reduced effective DNA charge density.
Moments of the distribution of the amino acid residues in tertiary structures of globular proteins
Authors: De Santis P. , Morosetti S. , Palleschi A. 
Published: December 2004

AbstractMoments of the distributions of the Cα and “side‐chain atoms” and associated properties were examined in 22 globular proteins, considered as statistical aggregates of atoms. Although the distributions are generally anisotropic, the densities of the evaluated distributions are highly uniform in the interior of a single protein, as well as among the proteins investigated. The tertiary structure of proteins is characterized by a compact and uniform distribution of amino acids, independent of their molecular weight and hydrophobic character, and by an isotropic distribution of the virtual bond directions in the polypeptide folding. While the general uniformity of the density of distributions in the bulk of proteins can be justified by the architectural requirements of high thermodynamic stability, significant differences in the distribution of the Cα with respect to the “side‐chain atoms” suggest a plausible explanation of the general anisotropic morphology of the proteins. The invariance of the density of distributions allows easy recognition of proteinlike domains in more complex proteins and suggests a practical way to predict the following path in single proteins.
Role of the amino‐terminal extrahelical region of type I collagen in directing the 4D overlap in fibrillogenesis
Authors: Helseth Donald L. , Lechner Joseph H. , Veis Arthur 
Published: December 2004

AbstractThe amino‐terminal telopeptide of the collagen α1(I) chain has a highly conserved sequence. This sequence was analyzed by the Chou‐Fasman criteria, and a folded β‐sheet conformation, including a β‐turn, was predicted. This folded “hairpin” region favors both ionic and hydrophobic intermolecular interactions with α1(I) chain residues 930–938 on a neighboring, end‐overlapped molecule. An end‐overlap interaction of this nature could direct the initial step in fibril formation. The predicted structure also places the potential crosslink‐forming lysyl residue, 9N, in a unique site at the β‐turn end of the telopeptide.
DNA sequencing and helix–coil transition. I. Theory of DNA Melting
Authors: Azbel M. Ya. 
Published: December 2004

AbstractAn explicit analytic formula accurately describing the melting of a natural DNA is derived. For phage ϕX‐174 and virus SV‐40, the nucleotide sequences of which are known, the formula fits experimental data for the differential melting curve almost within the experimental accuracy.