bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deuterium NMR and EPR of hydrated collagen fibers in the presence of salts
Authors: Fung B. M. , Trautmann Patricia 
Published: December 2004

AbstractA new model for hydrated collagen fibers is postulated. According to this model, a part of the water adsorbed is bound to the collagen fiber through hydrogen bonding, and the rest is randomly reorienting. The two types of water are in chemical exchange. The observed dipolar splitting for H2O and quadrupolar splitting for D2O are time‐averaged values. The deuterium quadrupole splitting of D2O in oriented collagen fibers decreases in the presence of salt. The phenomenon can be explained either by a change in the structure of collagen or by the blocking of the water binding sites by the ions. In the EPR spectra of collagen presoaked in Mn(II) and Cu(II) sulfates, the line widths decrease with the increase of water content, indicating the coordination of the cations to water. The change in the hyperfine splitting (from 70 gauss in dry fibers to 96 gauss in fibers equilibrated at 100% RH) of Mn(II) with water content is explained by the change in the symmetry of its environment.
Kinetic and hydrodynamic studies of the complex of proflavine with poly A·poly U
Authors: Schmechel D. E. V. , Crothers D. M. 
Published: December 2004

AbstractRelaxation kinetic experiments reveal general similarity between the mechanism of binding of proflavine to poly A·poly U and DNA. There are differences in detail, however. For example, the rate constants are roughly an order of magnitude smaller for the former, and the thermodynamic parameters of the individual steps are also different. The total heat and free energy for intercalation of free dye are quite similar in the two cases. As was the case with DNA, considerable dye (up to 25% of the bound form) is attached externally to the double helix, even in the strong binding region of the isotherm. Sedimentation measurements on small, rodlike fragments of poly A·poly U reveal a length increase on binding proflavine of a magnitude similar to that found with DNA. This length increase seems to become smaller under conditions (high temperature) where the relaxation measurements indicate a higher fraction of externally bound dye.
Conformational studies on concentrated solutions of poly(γ‐benzyl L‐glutamate)
Authors: Puett D. , Ciferri A. 
Published: December 2004

AbstractWe have studied the effect of polypeptide concentration on the helix–coil transition of poly(γ‐benzyl L‐glutamate) (PBLG) in both dichloroacetic acid (DCA) and DCA–chloroform (CHF) mixtures. In agreement with other reports, we find the van't Hoff transition enthalpy to be strongly dependent on PBLG concentration. Also, an apparent effect of polypeptide concentration was noted on the transition temperature; however, corrections for finite PBLG concentration on the mole fraction of DCA seem to remove this effect. In order to explain our data, as well as some calorimetric data in the literature, we consider the transition free energy and enthalpy as a sum of three partial terms. These represent the thermodynamic parameters associated with: (1) conformational changes of the polypeptide, e.g. formation or disruption of intramolecular hydrogen bonds; (2) binding by the strong acid to the nonhelical segments of the polypeptide; (3) an overall (weak) interaction of the polypeptide with the nonbound solvent giving rise to dilution parameters that are dependent on the polypeptide conformation. The latter effect is generally ignored, since it is assumed that solvent interactions, other than specific binding, are similar for both the helical and the nonhelical conformation. Striking effects of water (small amounts) and solution aging on the formation of PBLG helices was observed. Water, as expected, acts as a helicogenic solvent when combined with DCA. The processes occurring during solution aging are not known, although the net effect is to stabilize the helical conformation. Finally, we present some rather unique thermally induced transitions of concentrated PBLG (about 200 mg/ml) in DCA. At low temperatures the soluble randomly coiled conformation is present. Heating produces first an isotropic gel, followed at higher temperatures by an isotropic solution consisting of about 70% α‐helicity.
Binding of alcohols to the peptide CO group of poly‐L‐proline in the I and II conformation. II. Binding constants from infrared measurements in solution
Authors: Strassmair H. , Engel J. , Knof S. 
Published: December 2004

AbstractTrifluoroethanol, benzyl alcohol, and n‐butanol bind to the peptide and acelyl CO groups of poly‐O‐acetyl‐L‐hydroxyproline in dichloromethane via hydrogen bonds. The binding aflinity decreases from trifhioroelhanol to n‐buitanol. For the acelyl CO groups the binding does not depend on the conformation of the polymer but for the peptide CO groups the binding constants are larger by a factor of two to five time when it is in the helix II conformation (all peptide bonds trans) than when it assumes the helix I conformation (all peptide bonds cis). This preference is explained by the higher accessibility of the peptide CO groups in the II helix. The small additional energy which results from the preferential binding is sufficient, to induce a complete I → II transition because of the very high cooperativily of the system. The quantitative dependence of the equilibrium constant s for the propagation step of the transition on solvent composition (ratio of trifluoroethanol or benzyl alcohol to n‐butanol) is derived from the binding data. It agrees satisfactorily with the empirical relation obtained from a best fit to transition curves of Ganseret al. The I ⇌ II conversion of poly‐L‐proline is therefore an example of a conformational transition whose solvent dependence can be explained by a binding mechanism.
The crystal structure of the 2:1 intermolecular complex containing 1‐melhyl‐5‐flourouracil and 9‐ethyl‐2,6‐diaminopurine
Authors: Chandross Ronald , Rich Alexander 
Published: December 2004

AbstractTwo molecules of 1‐methyl‐5‐fluorouracil complex with one molecule of 9‐erthyl‐2, ‐6‐diaminopurine and crystsallize in a triclinic unit cell. The crystal structure was solves by analysis of 3‐dimensional x‐ray diffraction data. Asharpened Patterson map was used to dertermine the structure with apsuedo‐heavy atom technique. The three molecule from a planar hydrogen bonded Watson‐Crick pair with the purine while the other pyrimide forms hydrogen bond to adenine through the imdazole nitrogen. The network is compeleted by purine‐purine hydrogen bond.
Density‐gradient sedimentation equilibrium of DNA and the effective density gradient of several salts
Authors: Schmid Carl W. , Hearst John E. 
Published: December 2004

AbstractThe various treatments of sedimentation equilibrium are compared on a theoretical and an experimental basis. Particular attention is paid to the polyelectrolyte nature of the problem and the choice of a neutral component. The effective density gradients of several cesium salts for DNA are measured. Two previous theories for the effective density gradient are shown to be equivalent, and the experimental values are interpreted with respect to these theories. It is clear t hat sedimentation equilibrium in a density gradient may be used for the determination of unambiguous molecular weights.
Cooperative nonenzymic base recognition II. thermodynamics of the helix‐coil transition of oligoadenylic + oligouridylic acids
Authors: Pörschke Dietmar 
Published: December 2004

AbstractThe properties of oligonucleotide helices of adeuylic‐ and uridylic acid oligomers have been investigated by measurements of hypo‐and hyperchromieity. High ionic strengths favor the formation of triple helices. Thus, the double helix‐coil transition can be studied (without interference by triple helices) only at low ionic‐strength. A “phase diagram” is given representing the Tm‐values of the various transitions at different ionic strengths for the system A(pA)17 + U(pU)17. Oligonucleolides of chain lengths <8 always form both double and triple helices at the nucleotide concentrations required for base pairing. For this reason the double helix‐coil transition without coupling of the triple helix equilibrium can only be measured for chain lengths higher than 7. Melting curves corresponding to this transition have been determined for chain lengths 8, 9, 10, 11, 14 and 18 at different concentrations. An increase in nucleotide concentration leads to an increase in melting temperature. The shorter the chain length the lower the Tm‐value and the broader the helix‐coil transition. The experimental transition curves have been analysed according to a staggering zipper model with consideration of the stacking of the adeuylic acid single strands and the electrostatic repulsion of tlip phosphate charges on opposite strands. The temperature dependence of the nucleation parameter has been accounted for by a slacking factor x. The stacking factor expresses the magnitude of the stacking enthalpy. By curve fitting xwas computed to be 0.7, corresponding to a stacking enthalpy of about S kcal/mole. The model described allows the reproduction of the experimental transition curves with relatively high accuracy. In an appendix the thermodynamic parameters of the stacking equilibrium of poly A and of the helix‐coil equilibria of poly A + poly U at neutral pH are calculated (ΔHA = −7.9 kcal/mole for the poly A stacking and ΔH12 = −10.9 kcal/mole for the formation of the double helix from the randomly coiled single strands). A formula for the configurational entropy of polymers derived by Flory on the basis of a liquid lattice model is adapted to calculate the stacking entropies of adenylic oligomers.
Investigations on spectra and orientation of dipole moments of uracil and thymine by electrochromism
Authors: Seibold K. , Labhart H. 
Published: December 2004

AbstractThe direction of the ground stale dipole moment with respect to the transition moment to the lowest excited singlet state as well as the dipole moment in this excited state could be determined from the influence of an electric field on the light absorption of uracil and thymine in solution. By making use of results on the orientation of the transition moment in the molecular framework, the orientation of the ground‐and excited‐state dipole moments can also be fixed and compared with theoretical predictions. The agreement is fair. The measurements show that in both compounds a weak band is hidden under the longest‐wavelength absorption band.
Kinetics of sedimentation in a density gradient
Authors: Dishon Menachem , Weiss George H. , Yphantis David A. 
Published: December 2004

AbstractTwo models of sedimentation in a density gradient are analyzed. The first is for sedimentation in cylindrical sector geometry and contains the assumption that diffusion can be neglected. The second treats sedimentation in a rectangular field and includes diffusion, although the boundaries are not treated exactly. In both of these models we approximate the time dependence of the gradient by a relaxation form. We derive exact results for both models. It is also shown that the sedimentation coefficient can be calculated from data by following the motion of the position of the maximum (or minimum) of the concentration gradient.
Variation of the NH–CαH coupling constant with dihedral angle in the NMR spectra of peptides
Authors: Ramachandran G. N. , Chandrasekaran R. , Kopple Kenneth D. 
Published: December 2004

AbstractProton magnetic resonance data and conformational calculations of a series of model compounds containing a NH‐CαH group substituted as in peptides have been used to generate a proton–proton coupling constant–dihedral angle relation for the peptide unit. For those substances used in which the dihedral angle about the N‐Cα bond is not fixed, the angle distribution was calculated from conformational theory. Using eight examples in which the number of theoretical assumptions were least, the best values of the coefficients A, B, and C in the expression J(θ) = Acos2θ + B cosθ + Csin2θ were found by a least‐squares procedure to be 7.9, −1.55, and 1.35, respectively. This relation gives reasonable values for the dihedral angles ϕ in cyclic oligopeptide structures for which the availability of both NMR data and other structural information allow comparison. When applied to N‐acetylamino acid N‐methylamides having side chains extending beyond Cβ, however, agreement with the calculated conformational distribution was found for Leu, Met, and Trp, but observed values of J were larger than expected for Val, He, Phe, and Tyr, These disagreements are considered to be the result of interactions not yet taken into account in the usual conformational calculations.
Spectroscopic study of the self‐association of myosin
Authors: Herbert Thomas J. , Carlson Francis D. 
Published: December 2004

AbstractHomodyne and heterodyne measurements have been made of the spectrum and intensity of laser light scattered from solutions of skeletal muscle myosin at high salt concentrations. The spectral broadening and intensity measurements are consistent with the hypothesis that a myosin monomer‐dimer equilibrium exists in these solutions. Values have been calculated for molecular weight and radius of gyration of the myosin monomer, virial coefficients, and diffusion constants of both monomer and dimer, and equilibrium constant of the reaction to form dimer. Diffusion constant measurements yield an approximate length of 1481 Å for the monomer and 2121 Å for the dimer. The significance of these lengths is discussed in terms of the models of Huxley and Pepe for the structure of the myofilament.
β‐carbonylamides in peptide chemistry. II. Ultraviolet absorption and circular dichroic properties of azlactones derived from N‐acetoacetyl amino acids
Authors: Di Bello Carlo , Filira Fernando , Toniolo Claudio 
Published: December 2004

AbstractUltraviolet absorption and circular dichroism spectra of azlactones derived from N‐acetoacetyl amino acids are examined. A number of model compounds of the isomeric forms possibly present in the equilibrium mixtures of these azlactones have also been prepared and their spectral properties compared. The reported data permit, structural and stereochemical assignments on these amide compounds.
“Renaturation” des solutions cuivriques de DNA. I. Analyse phenomenologique
Authors: Richard H. , Pacault A. 
Published: December 2004

AbstractA study of the kinetics of renaturation of cupric DNA solutions has been carried out by two physical properties methods. The use of a purely phenomenological analysis leads nevertheless to interesting conclusions concerning the transformation mechanism. We have found that: in the presence of Cu++ ions, different. DNA samples exhibit an equivalent kinetic behavior; the system can be decomposed into two parts: DNA and copper ions, and the rate of formation of DNA should be faster than that of copper ions; the mechanism of transformation may be bimolecular, but further investigation is necessary to confirm this.
A non‐perturbation method for the optical properties of helical polymers
Authors: Loxsom F. M. , Tterlikkis L. , Rhodes William 
Published: December 2004

AbstractThe optical absorption and circular dichroism (CD) of poly‐L‐alanine in an α‐helical conformation are computed in terms of monomer properties by use of Bogoliubov exciton theory (a non‐perturbation method). It was shown earlier that a proper formulation of the theory of CD for large molecular systems permits the use of periodic boundary conditions, a feature which greatly simplifies calculations as well as conceptual understanding. If is found that the shape of the observed CD spectrum can be explained in terms of the two rotational strength components and an electric dipole strength component referred to as the helix term. Comparisons of the results of perturbation theory and Bogoliubov exciton theory show that perturbation theory is valid for absorption but is inadequate for CD if the coupling among monomers is sufficiently large lo predict the observed hypochromism.
The effect of adjacent charges on the kinetics of rotation of the peptide bond
Authors: Gerig J. T. 
Published: December 2004

AbstractThe kinetics of rotation of the peptide (amide) bond in dimethylacetamide, glycine dimethylamide, N‐acetylsarcosine, and glycylsarcosine have been studied in basic, neutral, and acidic aqueous solutions by proton magnetic resonance spectroscopy. The data indicate that the presence of nearby negative or positive charges do not greatly perturb the energetics of conformational equilibration about the amide carbon‐nitrogen bond. In N‐acetylsarcosine and glycylsarcosine two distinguishabe conformers are present; their relative abundance is essentially 50%/50% except at low pH. It is suggested that intramolecular hydrogen bonding is responsible for deviations from this population ratio. The activation enthalpies (ΔH‡) for rotation appear to be linearly related to the corresponding activation entropies (ΔS‡) leading to an isokinetic temperature of about 400°K.
Light scattering and hydrodynamic properties of linear and circular bacteriophage lambda DNA
Authors: Dawson J. R. , Harpst J. A. 
Published: December 2004

AbstractLow‐angle light scattering, sedimentation velocity, and intrinsic viscosity measurements have been made on circular and linear forms of lambda (λ) bacteriophage DNA. Available equations, used to relate hydrodynamic parameters of both forms to the molecular weight, give relatively consistent values of particle weights which essentially agree with the light‐scattering results. An average molecular weight of (34 ± 3) × 106 for λ DNA was obtained in good agreement with literature values of (31–33) × 106. The linear λ DNA has a larger root‐mean‐square radius than the circular molecule, when determined by light scattering, but the difference does not appear to be us large as expected from hydrodynamic data. The two forms also show significantly different angular distrbutions of scattered light intensities which agree only qualitatively with those derived from existing theory. The light‐scattering results suggest that further experiments and modifications of available theories should be undertaken.
Poly(γ‐p‐nitrobenzyl‐L‐glulainate): synthetic aspects, sedimentation, and viscosity studies
Authors: Feyen J. , De Groot K. , De Visser A. C. , Bantjes A. 
Published: December 2004

AbstractA series of poly(γ‐p‐nitrobenzyl‐L‐glutamates), PNBG, has been synthesized by the polymerization of N‐carboxyanhydride (NCA) derivatives of γ‐p‐nitrobenzyl‐L‐glutamate, NBG, using triethylamine as an initiator. We studied the influence of (a) the solvents dioxane, nitrobenzene, dimethylformamide (DMF), and DMF–1,2‐dichloroethane mixture and (b) the anhydride–initiator ratio (A/I) for the polymerization in nitrobenzene (A/I varying from 50 to 750) on the properties of the polymers obtained. In order to improve its synthesis, NBG, was prepared by three different methods. Ten samples of PNBG, ranging in Mw from 10,000 to 50,000, were examined viscometrically in DMF and dichloroacetic acid (DCA) and by ultracentrifugation in DMF. The data for [η] and So (limiting sedimentation coefficient) as functions of Mw for PNBG in DMF were utilized, applying theories of Kuhn and Kuhn,13 Schachman,14 and Perrin, 15 for the estimation of the length per monomeric residue h. Viscosity data gave a h value of about 2.3 Å, Whereas sedimentation yielded 1.5 Å. Treating viscosity and sedimentation data for poly(γ‐benzyl‐L‐glutamate), PBLG, in the same way leads to somewhat higher hvalues (2.4 Å and 1.7 Å, respectively).Although a nitroaromatic effect was shown to be absent for PNBG in DMF, it can be concluded that in this medium PNBG has a somewhat more compact structure than PBLG.
Magnetic circular dichroism study on synthetic polynucleotides, bacteriophage structure, and DNA's
Authors: Maestre Marcos F. , Gray Donald M. , Cook Randall B. 
Published: December 2004

AbstractThe MCD (magnetic circular dichroism) spectra of Ap, ApA, ApApA, poly A, Up, UpU, poly U and double‐stranded poly A:U alternating copoly A–U and alternating deoxyribopoly A–T were measured with a Cary 61 spectropolarimeter fitted with a Varian superconducting magnet at a field strength of 50 Kgauss. The MCD spectra of T2 and T5 DNA at various stages of heal denaturation were measured as a function of hyperchromicity of the sample. MCD spectra of the intact and degraded T2 and T5 phages were used to study the degree of alteration of the DNA inside the phages versus the DNA in vitro. The results for the adenine polymers show that the main MCD bands, B2u(271 nm), B1u(252 nm), and E1u(212 nm), show a decrease in specific magnitude as the length of the polymer is increased, reflecting the degree of stacking of the polymer. In contrast, the uridine series of polymers shows little change of the MCD bands, indicating that there is little interaction between the bases regardless of the length of the polymers. The MCD spectra of poly A:U, alternating poly r(A–U): (A–U), and alternating poly d(A–T):(A–T) show significant differences among themselves in the magnitude of the B2u band and when compared with the sum of the spectrum for the poly A plus poly U. This may indicate the selective effect of hydrogen bonding on the B2u band. Alternatively, the difference may be due to the absence of an n → π* transition in the double‐stranded polymer. Measurements of denatured T2 and To DNA's show increases in all MCD bands. The T2 DNA internally packed in phage shows an increase of the B2u and E1ubands, the B2u remaining unchanged. The internal T5 DNA shows an increase of the B1u band only. Thus, the internal DNA structure is altered in a manner quite different from a simple denaturation caused by hydrogen bond breaking. Furthermore, different MCD bands indicate that different modes of DNA packing exist for T2 and T5 phages.
An infrared study of unordered poly‐L‐proline in CaCL2 solutions
Authors: Johnston Nancy , Krimm S. 
Published: December 2004

AbstractInfrared spectra have been obtained of poly‐L‐proline in aqueous CaCl2 solutions. As the salt concentration is increased, the CO stretching band develops a component at the frequency found in the solid state while the CH2 bending band broadens to higher frequency. Since circular dichroism spectra indicate progressive disordering of the chain with increasing salt concentration, we associate the infrared spectral changes with the same phenomenon. Our interpretation of these changes, particularly in the CH2 bending modes, is that disordering is associated primarily with an increase in the range of accessible Cα–C′ (O) rotation angles rather than with the random introduction of cis imide bonds in the chain.
Evaluation of RNA conformation from circular dichroism and optical rotatory dispersion data
Authors: Gratzer W. B. , Richards E. G. 
Published: December 2004

AbstractAn analysis of optical rotatory dispersion and circular dichroism of RNA is described which leads to an estimate of the degree of base pairing. By the use of new standards for the double‐helical parts of the molecule, based on data for two‐stranded viral RNA species, a good fit between calculated and observed curves can be achieved. Where data are available the results of analyses of optical rotatory dispersion and circular dichroism in general show satisfactory consistency.