bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum‐mechanical study of the hypochromic effect in polynucleotides. Intra‐ and interstrand interaction contributions
Authors: Danilov V. I. , Volkov S. N. 
Published: December 2004

AbstractThe first uv absorption band hypochromism of poly(dA) · poly(dT), poly(dG) · poly(dC), poly(dA), poly(dT), poly(dG), and poly(dC) is calculated with the help of perturbation theory on the basis of monomer characteristics computed by the Pariser‐Parr‐Pople method taking into account all singly excited configurations. The theoretical results obtained are in good agreement with experimental values of hypochromism. The origin of the hypochromic effect in the double‐stranded polynucleotides is investigated. It is shown that intrastrand interactions between the bases make the main contribution to hypochromism (60–76%), while the contribution of the Watson–Crick‐pair formation is small (2–12%). The essential part of hypochromism (22–28%) is due to the interstrand interactions between the bases that are not coupled by hydrogen bonds. The discussion of the experimental data shows that the present theoretical investigation could serve as a basis for the correct treatment of experimental data.
Carbon‐13 and proton nmr studies of helix–coil transition of poly(γ‐benzyl‐L‐glutamate)
Authors: Suzuki Yasuyuki , Inoue Yoshio , Chûjô Riichirô 
Published: December 2004

AbstractThe helix–coil conformational transition undergone by poly(γ‐benzyl‐L‐glutamate) in solutions of trifluoroacetic acid and deuterated chloroform was studied by proton and carbon‐13 nmr. The results indicate that in the case of the solvent‐induced helix–coil transition, the side chain assumes a helical conformation before the backbone. In the thermally induced helix–coil transition, the results indicate the existence of an intermediate state, which is between the α‐helix and random coil and is free from intramolecular hydrogen bonding.
Levans. II. Light‐scattering and sedimentation data of Streptococcus salivarius levan in water
Authors: Stivala S. S. , Bahary W. S. , Long L. W. , Ehrlich J. , Newbrun E. 
Published: December 2004

AbstractThe molecular weights and radii of gyration of Streptococcus salivarius levan fractions were obtained from light‐scattering measurements in water. Sedimentation coefficients and partial specific volumes of the fractions were also obtained. Double logarithmic plots of [η] versus M̄w and S0 versus M̄w yielded slopes having values of 0.17 and 0.62, respectively. The data and various calculated parameters show that levan from Streptococcus salivarius is highly branched and behaves hydrodynamically as a compact particle of spherical symmetry.
Base pairing of adenine and uracil derivatives in the presence of water
Authors: D'Albis Anne , Wickens M. P. , Gratzer W. B. 
Published: December 2004

AbstractThe association of chloroform‐soluble derivatives of uracil and adenine has been examined in chloroform solution in the presence of dissolved water. Analysis by infrared spectroscopy shows that complex formation still occurs in these conditions, and that the extent of association is substantially unchanged by the presence of water. Evidence is presented for the coexistence of two kinds of base pair (involving, respectively, the C2 and C4 carbonyl groups of the pyrimidine) in the solutions, and for some displacement in their relative balance by the added water. The binding of water to the C2 and C4 carbonyl groups can be separately observed in both the free uracil derivative and its 1:1 complex with 9‐ethyladenine. Little or no competition has been found to occur between the formation of base pairs and binding of water to the bases, as judged by measurements of water solubility in chloroform solutions of the bases individually and in 1:1 mixtures. The evidence suggests that this phenomenon can be largely explained by the formation of double hydrogen bonds by the uracil carbonyl groups. Taken together with recent published observations, the results indicate that hydrogen bonding may make a much greater energetic contribution to conformational stability of biopolymers in aqueous solution that has been supposed.
Electrofocusing of heparin: Fractionation of heparin into 21 components distinguishable from other acidic mucopolysaccharides
Authors: McDuffie Norman M. , Dietrich Carl P. , Nader Helena B. 
Published: December 2004

AbstractTwenty‐one fractions have been demonstrated in each of 15 different commercially available heparins subjected to electrofocusing. These fractions show a molecular‐weight range from 3000 to 37,500 with a constant interval between molecular weights. Degradation of each fraction by purified enzymes of Flavobacterium heparinum yielded identical end products, suggesting chemical identity. Only fractions with a molecular weight of 7000 and up had significant anticoagulant activities.The phenomenon of electrofocusing of mucopolysaccharides is dependent upon pH, molecular weight, and ampholyte availability. Chemical composition of the mucopolysaccharide is also an essential factor since N‐ and O‐desulfation of heparin markedly changed the focalization pattern.The pattern produced when heparin is subjected to electrofocusing is not duplicated by any other naturally occurring acidic mucopolysaccharide tested. Heparitin sulfate D shows some similarities to heparin and it is probable that heparitin sulfate D is a normal contaminant of heparin preparations (this assumption is supported by molecular‐weight and anticoagulant activity determinations).The technique is specific and reproducible and unequivocally distinguishes heparin from other acid mucopolysaccharides.
Influence of the sugar configuration on the structure of DNA by conformational analysis of the deoxyribose‐phosphate unit
Authors: Cornillon Raphaël , Lespinasse Jean‐Noël , Broch Henri , Vasilescu Dane 
Published: December 2004

AbstractThe conformational analysis by the Extended Hückel Theory of the deoxyribose‐phosphate unit in the principal configurations of the sugar is discussed. The work is divided into three parts in order to determine the role of the different elements constituting such a unit. (1) The simultaneous study, for the four principal configurations of the sugar, of the possible ranges of the rotational parameters ψ and ϕ′ with P3 and P5 without their oxygen atoms. (2) The study of the influence of the oxygen atoms, situated on P3 and P5, on the rotations ψ and ϕ′ for the C3′endo and C2′endo sugar configurations. (3) The study of the influence of a nucleobase on the rotation ψ, and whether the oxygen atoms of the phosphate groups should be taken into account or not.The results show the equivalences C3′endo ≃ C2′exo and C2′endo ≃ C3′exo; that the allowed angular ranges of our rotational parameters depend, in some degree on the chosen sugar configuration; and that the rotations ψ and ϕ′ appear as “quasi” independent. In addition, an energetic classification which, according to the Extended Hückel Theory, seems to show that the C2′endo sugar configuration is the most favored for our unit was established; it was shown that the introduction of the oxygen atoms has no influence on the rotation ψ, but on the contrary leads to a restriction of the possible range for the ϕ′ parameter; and it was determined that the influence of the adenine base fixed in its position of minimal energy (i.e., anti‐conformation) on the rotation ψ, as a function of the presence or absence of the oxygen atoms, is relatively limited.
Analyse conformationnelle de la N‐méthylamide de l'acide L‐pyroglutamique par diffusion Rayleigh depolarisée, spectroscopie de vibration et calcul de l'energie conformationnelle
Authors: Allard Michèle , Avignon Michel , Bellocq Anne‐Marie 
Published: December 2004

AbstractConformational analysis of N‐methylamide of pyroglutamic acid has been performed by theoretical energy calculations and experimental physical techniques, namely, laser Raman spectroscopy and depolarized Rayleigh scattering. The two theoretically predicted conformations are evidenced in crystalline state (ψ1 = +169°) and in aqueous solution (ψ1 ≃ −20°). This study confirms the interest of a careful vibrational analysis of peptides and N‐deuterated derivatives for providing an estimate of the dihedral angle ψ. The relationship between amide III frequency and ψ values is emphasized.
Refinement of the structure of β‐chitin
Authors: Gardner K. H. , Blackwell J. 
Published: December 2004

AbstractThe structure of β‐chitin has been refined by rigid‐body least‐squares methods, based on the intensity data for highly crystalline specimens from the pogonophore Oligobrachia ivanovi. The structure consists of an array of poly‐N‐acetyl‐D‐glucosamine chains all having the same sense, which are linked together in sheets by NH … OC hydrogen bonding of the amide groups. In addition to the O‐3′H … O‐5 intramolecular hydrogen bond, analogous to that in cellulose, the CH2OH side chain forms an intrasheet hydrogen bond to the carbonyl oxygen on the next chain. This structure shows considerably better agreement between observed and calculated intensities than that possessing an intersheet hydrogen bond, as had been proposed previously. The structure is consistent with the swelling properties of β‐chitin and can also be seen to be analogous to that of native cellulose.
Conformational analysis of polynucleotide chains. Double‐stranded structures
Authors: Calascibetta F. G. , Dentini M. , De Santis P. , Morosetti S. 
Published: December 2004

AbstractConformational analysis of double‐stranded helical polynucleotides was carried out in terms of internal and external parameters, using semiempirical energy potential functions. The results obtained show that the structures proposed on the basis of the X‐ray analysis for A‐DNA and RNA's are almost identical to those corresponding to the conformational energy minima, whereas that proposed for B‐DNA still appears to suffer from conformational strains. On the other hand, the B‐DNA structure theoretically predicted is stabilized by both van der Waals energy and possible specific interactions with water molecules and counterions. This may explain the stability of the B form with respect to the A form at high relative humidity and ion strength. A possible role of the A + T fraction in stabilizing the B‐type DNA emerges in connection with its preferential ability to bind ions. This agrees with the results on the crystalline structures of GpC and ApU. For RNA's, the occurrence of only A‐type structures is explained as being due to the C(3′)‐endo puckering of ribose in a double helix.
Poly(L‐valine). Conformational dependence on the degree of polymerization: Infrared studies
Authors: Itoh Koichi , Fasman Gerald D. 
Published: December 2004

AbstractThe infrared spectra of poly(L‐valine)'s with varying degrees of polymerization have been investigated, as well as copolymers of L‐alanine and L‐valine. The spectra of nujol mulls of various molecular‐weight poly(L‐valine)'s, isolated directly from the polymerization media, as well as spectra of these same samples after treatment with strong acid, are recorded. In the 700–250‐cm−1 region, bands at 543 and 414 cm−1 are found to increase with increasing degree of polymerization in the nujol mulls, but are missing in the acid‐treated samples. These bands are assigned to the L‐valine residues with an β‐helixlike local conformation. It is inferred that the polymerization proceeds initially in the β form, and after a critical degree of polymerization the chains adopt an appreciable amount of an α‐helixlike local conformation.
Reversible structural changes in a hydrophobic protein, elastin, as indicated by fluorescence probe analysis
Authors: Gosline John M. , Yew Foch F. , Weis‐Fogh Torkel 
Published: December 2004

AbstractFluorescent probe analysis of purified elastin using 1‐anilinonaphthalene‐8‐sulfonate has been used to investigate reversible structural changes that accompany stretching of this rubberlike protein. There is a specific binding of 1‐anilinonaphthalene‐8‐sulfonate to elastin with a single dye molecule attached per 74,000 molecular‐weight protein subunit. When labeled elastin is stretched, the intensity of the 1‐anilinonaphthalene‐8‐sulfonate fluorescence decreases reversibly, and this decrease appears to be linked to an increase in the environmental polarity in the immediate vicinity of the bound dye molecule. The results of experiments carried out in H2O and D2O indicate that this polarity change is due to an increase in the exposure of the 1‐anilinonaphthalene‐8‐sulfonate to water as the hydrophobic interior of the protein subunit is unfolded during stretching. The data are consistent with the proposal that the elastin network is a two‐phase system of hydrophobic protein globules surrounded by free solvent spaces.
Conformation of histidine model peptides. III. Chiroptical properties of cyclo‐L‐alanyl‐L‐histidine and cyclo‐L‐histidinyl‐L‐histidine
Authors: Grebow Peter E. , Hooker Thomas M. 
Published: December 2004

AbstractThe chiroptical properties of the cyclic dipeptides cyclo‐L‐alanyl‐L‐histidine and cyclo‐L‐histidinyl‐L‐histidine have been investigated as a function of molecular conformation. The rotatory strengths of the n‐π* transitions of the peptide chromophores and the lowest energy π‐π* transitions of the imidazole chromophores have been calculated as a function of the angle of fold of the cyclic dipeptide group and the dihedral angles χ1 and χ2 of the amino acid side chains. The results of this investigation are consistent with the preferred position of the dihedral angle χ1 occurring near 60° in the free base form of cyclo‐L‐alanyl‐L‐histidine, and near 180° when the imidazole side chain is protonated. Furthermore, in the case of the free base form of the imidazole group, it is possible that the tautomeric isomer in which Nε is protonated may be more prevalent than the isomer in which Nδ is protonated.
Infrared and Raman spectroscopy of carbohydrates. Part VI: Normal coordinate analysis of V‐amylose
Authors: Cael John J. , Koenig Jack L. , Blackwell John 
Published: December 2004

AbstractA normal coordinate analysis of V‐amylose has been performed for an isolated 61 helical chain. Negligible splitting from interactions of vibrations of successive residues is expected between A and E vibrational species due to the large size of the monomer unit. As a result, calculation of only the totally symmetric A modes represents an adequate approximation to the vibrational spectrum of helical polysaccharides. Using this method together with a valence force field we have obtained good agreement between the observed and calculated frequencies. In addition, the computed potential energy distribution and Cartesian displacement coordinates match previous experimental assignments, based on deuterium exchange. The analysis also supports the proposed mechanism for conversion of V‐amylose to the more extended B‐form. This conversion results in an observed frequency shift for the Raman line at 946 cm−1 which is predicted by the calculations.
Ordered forms of 5′‐8‐aminoguanylic acid
Authors: Hattori Masao , Frazier Joe , Miles H. Todd 
Published: December 2004

Abstract5′‐8NH2GMP forms an ordered structure in moderately acid (pD 4.7) solution. We propose for this ordered form a novel hemiprotonated G·G structure with a twofold rotation axis and three hydrogen bonds between each pair of guanine residues. Gel formation does not occur with this nucleotide in either neutral or acid solution. In neutral solution 5′‐8NH2GMP also forms a regular, ordered structure, quite different from the acid form and similar to that formed by 5′‐GMP under the same neutral conditions. We suggest that this ordered structure consists of a regularly stacked array of planar tetramers, similar to that proposed for 3′‐GMP at pH 5.2
Backbone conformations in deoxyribonucleic acids. Conformational role of the 2′‐hydroxyl group on the internucleotide phosphodiester conformations
Authors: Yathindra N. , Sundaralingam M. 
Published: December 2004

AbstractThe conformations accessible to the internucleotide phosphodiester group in deoxydinucleoside monophosphates, deoxydinucleoside triphosphates, and deoxypolynucleotides have been explored in detail by potential energy calculations. The two most predominant conformations for the nucleotide moiety (3E and 2E) and their possible combinations (3E−3E, 3E−2E, 2E−2E, 2E−3E) have been employed, similar to our earlier studies on polyribonucleotides. The internucleotide P‐O bond torsions are very sensitive to the sugar pucker (3E and 2E) and sugar type (ribose and 2′‐deoxyribose) on the 3′‐residue of dinucleoside phosphates. The preferred phosphodiester conformations found for the deoxydinucleoside monophosphates and triphosphates, in general, follow the same pattern as those obtained for ribose sugars when the sugar on the 3′‐side of the molecule has the 3E sugar‐ring conformation. The internucleotide P‐O bonds show a greater degree of conformational freedom when the 3′‐sugar has the 2E pucker. The double gauche g−g− conformation for the phosphodiester, which leads to the overlap of the adjacent bases, is shown to be one of the energetically most favored conformations for all the sequence of sugar puckers. It is found that the 2E−2E sequence of sugar puckers shows a greater energetic preference for the stacked helical conformation (g−g−) than the (3E−3E) and the mixed sugar‐pucker combinations. This effect becomes more pronounced in going from a dinucleoside monophosphate to a dinucleoside triphosphate suggesting that the 2′‐deoxy sugars favor the 2E sugar pucker in di‐, oligo‐, and polydeoxyribonucleotide structures. In addition to g−g−, the conformations g+g−, tg−, g−t, tg+, and g+t are also found to be possible for the phosphodiester in a polydeoxyribonucleotide and their populations depend to some extent on the sugar‐pucker sequence. It is shown that the short‐range intramolecular interactions involving the sugar and the phosphate groups dictate to a large extent the backbone conformations of nucleic acids and polynucleotides.
Influence of Mn2+ ion coordination on tRNAVal1 macrostructure and determination of some coordination sites of Mn2+ ions in tRNAVal1
Authors: Vocel S. V. , Slepneva I. A. , Backer J. M. 
Published: December 2004

AbstractElectron paramagnetic resonance spectroscopy has been used to study the coupling of Mn2+ ions with the tRNAVal1 modified with a spin label at four pseudouridylic residues and with the valyl‐tRNAVal1 modified with a spin label at the α‐amine group of the valyl residue. A sharp increase of spin‐label mobility has been found in these samples, due to the conformational transition induced by the first and second Mn2+ ions. Analysis of dipole–dipole couplings of spin labels with the coordinated ions revealed a definite order in the occupation of ion coordination sites in the tRNA. For some valyl‐tRNAVal1 molecules, the second Mn2+ ions were shown to coordinate on the α‐amine group of the valyl residue at a distance of 15–25 Å from a spin label. As a result of the conformational transition, a coordination site appeared in the tRNA at one of the pseudouridylic residues, its distance from the spin label being less than 10 Å. It has been suggested that the conformational transition induced by ions excluded some bases from the system of hydrogen bonds at the level of the tRNA tertiary structure. As a result, these bases acquired sufficient sterical freedom to participate in the Mn2+ ion coordination.
Levans. III. A light‐scattering study of Streptococcus salivarius levan in dimethyl sulfoxide
Authors: Bahary W. S. , Stivala S. S. , Newbrun E. , Ehrlich J. 
Published: December 2004

AbstractA light‐scattering study of unfractionated and five fractions of Streptococcus salivarius levan was performed in dimethyl sulfoxide. The weight‐average molecular weights M̄r in dimethyl sulfoxide, after adequate dissolution, agree with those obtained in water within a mean difference of 7%. The intrinsic viscosities [η] and root‐mean‐square z‐average radii of gyration (Rg2)z1/2 are significantly higher in dimethyl sulfoxide than in water, reflecting the higher hydrodynamic volume in the former. The M̄r, [η], and (Rg2)z1/2 of the fractions suggest that levan has a low polydispersity. The exponent of 0.12 of the Mark‐Houwink plot and model analysis confirm the branched and compact structure of levan.
Polarized fluorescence in an electric field. A model calculation with application to the geometry of the 2‐hydroxy‐4,4′‐diamidinostilbene–DNA complex
Authors: Weill G. , Sturm J. 
Published: December 2004

AbstractTheoretical expressions are derived for the change in the polarized components of the fluorescence, resulting from the orientation of a rigid molecule bearing a chromophore with arbitrary angles for the absorption and transition moments \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _a $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _e $\end{document} with respect to the molecular axis. The break in the symmetry relation HV = VH is related to the tilt angle between \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _a $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _e $\end{document}. The theory is applied to a sonicated DNA–2‐hydroxy‐4,4′‐diamidinostilbene complex, in the blue and red emission bands of this peculiar dye. Simultaneous measurements of linear dichroism and fluorescence lead to the determination of an angle of 47° between a fluorescent bound dye and the DNA axis, with no difference for the blue‐ and red‐emitting species, but confirm the presence of nonfluorescent bound dye in a more perpendicular arrangement.
Irreversible thermodynamic analysis of electrophoretic light scattering experiments
Authors: Friedhoff L. , Berne B. J. 
Published: December 2004

AbstractA fluctuation theory for electrolyte solutions is developed based on the coupling between the equations of nonequilibrium thermodynamics and the Poisson equation. The resulting fluctuation theory is applied to the analysis of electrophoretic light scattering. It is shown that in a binary electrolyte solution (two ionic species), the Doppler shift is not determined by the electrical mobility of either ion, but depends instead on the rate of change of transference number with salt concentration. In addition the ionic relaxation time is shown to be proportional to the conductivity of the solution.
Application of the nearest‐neighbor ising model to the helix–coil transition of polypeptides in mixed organic solvents
Authors: Cabani S. , Paci A. , Rizzo V. 
Published: December 2004

AbstractUsing the formalism of nearest‐neighbor Ising model and assuming that the allowed states for a monomeric unity of a polypeptide chain in solutions containing strong acids are E (helix), C (coil), and CS (solvent‐bonded coil), the partition function of the system was deduced analytically. Equations were obtained which permitted the prediction of the characteristic thermodynamic behavior of the helix–coil transition under these conditions. These equations were used to examine critically the possible correlations between experimental data obtained using different techniques. Particular attention was devoted to quantities called “transition enthalpies,” obtained from the slope of the transition curves at the point where the helix fraction is one‐half (ΔH), or for measurements of the heat of solution of the polymer over the total range of solvent composition (ΔH), or from heat capacity measurements taken at various temperatures (ΔH). Literature data of ΔH(j = opt, sol, cal) for the system poly‐γ‐benzyl‐L‐glutamate in mixtures of dichloroacetic acid and 1,2‐dichloroethane were carefully analyzed.