bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acoustical properties of aqueous solutions of oxygenated and deoxgenated hemoglobin
Authors: Schneider F. , Müller‐Landau F. , Mayer A. 
Published: May 2005

AbstractThe acoustical relaxation spectrum of aqueous solutions of oxygenated and deoxygenated hemoglobin solutions was investigated in the frequency range 0.5–1000 MHz. The abrupt high frequency cut off of the broad absorption spectrum is consistent with a heavily weighted, shortest relaxation time of 2 × 10−9 sec. Both the high‐frequency cut‐off and high frequency residual absorption appear to be slightly different for oxygenated and deoxygenated hemoglobin solution.
Spectroscopic properties of oligonucleotides excised from the anticodon region of phenylalanine tRNA from yeast
Authors: Maelicke Alfred , Haar Friedrich Von Der , Cramer Friedrich 
Published: May 2005

AbstractUltraviolet absorption and static fluorescence properties of hexanucleotide (Gm‐A‐A‐Y‐A‐ψp) and a dodecanucleotide (A‐Cm‐U‐Gm‐A‐A‐Y‐A‐ψ‐m5C‐U‐Gp) excised from the anticodon region of phenylalanine tRNA from yeast have been studied with respect to temperature, pH, ionic strength, and Mg2+ concentration. At low temperature these oligomers have a largely stacked structure. Only the melting data of the dodecanucleotide in absence of Mg2+ fit a two‐state model. From the different melting behavior of the oligonucleotides after excision of base Y, a rodlike structure of the hexanucleotide produced by stacking interactions can be concluded. The Y fluorescence increase produced by Mg2+ has been used to evaluate the binding equilibria between Mg2+ and the oligonucleotides. One strong binding site per oligonucleotide and a greater number of weak binding sites have been found. The fluorescence of the free base Y is not influenced by Mg2+. The dodecanucleotide enhances the ethidium fluorescence to the same extent as tRNAPhe and produces comparable shifts in the excitation and emission spectra. Therefore a double helical structure for this oligomer under the assay conditions is suggested. Only weak binding of ethidium to the hexanucleotide is observed, indicating that intercalation of the dye into its structure is not favored. The data show the decisive role of the nucleobase Y in maintaining a rigid stacked structure of the anticodon nucleotides. This structure is stabilized by high ionic strength, Mg2+, and ethidium.
Conformational analysis of an ionizable polydipeptide
Authors: Hiltner W. A. , Hopfinger A. J. , Walton A. G. 
Published: May 2005

AbstractA semi‐empirical conformational energy calculation has been performed on the ionizable polydipeptide poly(Glu‐Ala). The results indicate that; (1)the ionized polymer assumes the lefthanded extended helix conformation is aqueous solution; (2) the poly(Glu‐Ala) extended helix is less stable than that of polyglutamic acid; (3) the unionized polydipeptide will preferentially assume the “β‐helical” conformation (isolated 21 degenerate helix) in aqueous solution. These conclusions are supported by experiment.
Effect of degree of polymerization and steric configuration of poly(2‐vinylpyridine) as catalyst in the polymerization of phenylalanine NCA
Authors: Imanishi Yukio , Nagaoka Shoji , Suzuoki Kazuhiro , Higashimura Toshinobu 
Published: May 2005

AbstractDespite its being weaker base poly(2‐vinylpyridine) polymerized DL‐β‐phenylalanine NCA at a much faster rate than pyridine and α‐picoline. Poly(2‐vinylpyridine) adsorbs NCA by hydrogen bonding with the cooperation of a few pyridine groups. This results in a high local concentration of NCA. The syndiotactic configuration of pyridine group seemed to be least suitable for the cooperative hydrogen bonding. Adsorbed NCA is activated to form an “activated” NCA which in turn reacts with an NCA adsorbed on the same polymer chain. Since the polymer chain is flexible, this intramolecular reaction takes place frequently, resulting in the acceleration of polymerization. The intramolecular reaction along the polymer chain is dependent on the degree of polymerization of polymer catalyst. A suitable model was proposed for the intramolecular reaction to explain the effect of degree of polymerization.
The conformational characteristics in solution of the synthetic cyclic hexapeptide
Authors: Tonelli Alan E. , Brewster A. I. Richard 
Published: May 2005

AbstractAn attempt to elucidate the solution conformation(s) of the synthetic cyclic hexapeptide 5L‐ala·D‐ala is described. Nuclear magnetic resonance (nmr) spectra are recorded for the purpose of measuring the vicinal coupling constant between the amide and α‐protons in each residue and to observe the deuterium exchange rate and temperature dependence of the chemical shift of each amide proton. Low‐energy cyclic conformations, whose individual residues are in conformations consistent with the observed amide to α‐proton coupling constant, are searched for in an approximate theoretical treatment. The two lowest energy, all trans peptide bond conformations generated are distinguishable by the presence or absence of a single intramolecular hydrogen bond. The observed temperature independence of the chemical shift of one of the amide protons is consistent with the presence of a single intramolecular hydrogen bond, while the observation of similar deuterium exchange rates for each of the amide protons indicates their comparable availability to solvent. Consequently, it is concluded that 5L‐ala·D‐ala is in rapid equilibrium between conformations with and without a single internal hydrogen bond and possesses considerable conformational flexibility in solution.
Origins of the differences between the circular dichroism of DNA and RNA: Theoretical calculations
Authors: Moore Dexter S. , Wagner Thomas E. 
Published: May 2005

AbstractTheoretical calculations of the circular dichroism of double‐helical DNA and RNA by the method of Johnson and Tinoco were performed in order to investigate the origins of the optical activity spectral differences between these polynucleotides. Calculations were performed using transition moment directions arising from molecular orbital calculations as well as a transition moment directions in agreement with experimental directions. The results of these calculations indicate that the conservative circular dichroism spectrum of B‐form DNA and the nonconservative spectrum of RNA (and A‐form DNA) arise as a consequence of the distance between the paired bases and the helix axis. The negative nonconservative spectrum of C‐form DNA was calculated and shown also to result from the distance of the paired bases from the helix axis. Several other conspicuous geometric parameters of DNA and RNA were investigated and were found to be less significant in their effects upon the spectral differences. Theoretical calculations on a four‐stranded DNA model which has paired bases similarly related to the helix axis as RNA and A‐form DNA was found to yield a low intensity, nonconservative circular dichroism spectrum.
Etude Potentiométrique de l'α‐Poly(acide‐L‐glutamique) et de ses Oligomères. II
Authors: Rinaudo M. , Domard A. 
Published: May 2005

AbstractPotentiometric neutralization of oligomers represented by the general formula shown was studied.
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The intrinsic pK of carboxyl function was found to be 4.40 at 25°C; the variation of the apparent pKa, ΔK(α), was studied as a function of the degree of neutralization: the influence of the degree of neutralization on the accumulation of ionic sites along the chain is clearly shown.The experimental curves of polyglutamic acid allowed us to deduce the sequence of ionic selectivity and the energy of conformational transition. The theoretical interpretation of the results was proposed in terms of the rod like model from Katchalsky's theory. The intrinsic pKo for the polymer was set equal to the value experimentally obtained on oligomers. By activity measurements on Na+ and Ca2+ counterions in salt‐free solutions, the free fraction of counterions was deduced on the different samples. The results were interpreted with the electrostatic model previously proposed; in this view, the oligomers are assimilated to imaginary polyelectrolytes. This allowed us to determine the values of ΔpK and the fraction of free ions at the same time.
Cooperative and thermodynamic parameters for oligoinosinate—polycytidylate complexes
Authors: Springgate M. W. , Poland Douglas 
Published: May 2005

AbstractThe cooperative nature of the binding between polycytidylate and the oligoinosinates I(pI)5–10 has been determined. Using the data of Tazawa, Tazawa, and Ts'o, it is shown that knowledge of the slope of the adsorption isothern allows one to determine the oligomer‐polymer binidng constant, the oligomer–oligomer interaction constant, and the average degree of association (cooperative clustering) of the oligomers on the polymer. Knowledge of the above equilibrium constants as a function of temperature yields the respective thermodynamic parameters; no assumptions need to be made about the nature of the equilibrium constants or the thermodynamic parameters. For very long chains of polycytidylate, simple, explicit relations are given for the determination of the equilibrium constants involved. For finite chains of polycytidylate, the calculation of a single graph for each oligomer and polymer size allows the equilibrium constants to be determined for all experimental conditions of temperature and concentration. We find that the enthalpy and entropy of binding an oligomer n, bases to be δHn = ±13.7 − n(6.65) and δSn = +32.5 − n(18.8) given, respectively, in kcal/mole and e.u.; these parameters predict a melting temperature of 81°C for the poly(I)·poly(C) complex compared with the experimental value of 75°C. If the enthalpy is interpreted as arising from a sum of hydrogen bonding and stacking interactions, then the enthalpy of stacking is −13.7 kcal/mole while the enthalpy of hydrogen bonding is +7 ± 4 kcal/mole; the positive enthalpy of hydrogen bonding presumably is a result of the fact that in the inosine‐cytosine base pair, only two of the three sites on cytosine can hydrogen bond, the third being blocked from hydrogen bonding with water. The enthalpy of interaction between neighboring bound oligomers is found to be −10.4 kcal/mole while the corresponding entropy is −26.1 e.u. The binding is bound to be cooperative, though the extent of clustering varies markedly with temperature; the average number of oligomers in a cluster on the polymer is found to about five at a melting temperature of 25°C. The approach and equations given have generally applicability to oligomer‐polymer associations.
Conformational studies on pyrimidine 5′‐monophosphates and 3′,5′‐diphosphates. Effect of the phosphate groups on the backbone conformation of polynucleotides
Authors: Yathindra N. , Sundaralingam M. 
Published: May 2005

AbstractIn continuation of our studies on the effect of the base and the phosphate groups on the glycosyl and the sugar‐phosphate backbone conformation, we have carried out semi‐empirical potential energy calculations on the common 5′‐ and 3′5′‐ribopyrimidine mono‐ and diphosphates by considering simultaneous rotations about the glycosyl (χ) and the C(4′)–C(5′) (ψ) bonds. This calculation provides an assessment of the nature and orientation of the base on the sugar–phosphate backbone conformation of nucleotides and polynucleotides. It is found that the attractive inetractions between the 5′‐phosphate group and the base mutually stabilize the antiand the gauche‐gauche (gg) conformations about χ and ψ, respectively, in 5′‐ribopyrimidine nucleotides. The introduction of the 3′‐phosphate group as in 3′,5′‐ribopyrimidine diphosphates, still leaves the anti‐gg as the most favored conformation with the important difference that the probability of occurrence of the anti, gauche‐trans (gt) is how substantially increased. This is dependent to a large extent on the sugar conformation and to a lesser extent on the base. Uracil and thymine show a greater probability for the anti‐gt than cytosine. The syn conformation is considerably less likely and its occurrence is also dependent on the base type, cytosine showing a lesser tendency than uracil and thymine. For the syn base, the most favourec conformation for ψ is gt, since gg is sterically disallowed and tg is destabilized by electrostatic repulsive interactions between the 3′ and 5′‐phosphate groups. Thus, there is a striking correlation between the glycoysl and the backbone C(4′)–C(5′) bond conformations. The rest of the bonds of the backbone are considerable less dependent on the glycosyl conformation. These studies reveal that in poly‐ribopyrimidine nucletides the majority of the nucleotide residues are expected to occur in the anti‐gg conformation.
Influence of isopropanol‐water solvent mixtures on the conformation of poly‐L‐lysine
Authors: Barteri M. , Pispisa B. 
Published: May 2005

AbstractThe helix–coil transition of poly‐L‐lysine (PLL) in water–isopropanol solvent mixtures has been investigated at room temperature by circular dichroism measurements. Within the range of 70%–80% isopropanol concentration (by volume), the polymer undergoes a sharp transition, characterized by the formation of a fully charged α‐helical structure. On the basis of some experimental evidence the role of the organic component in solution appears more complicated than that of strengthening the intramolecular hydrogen bonds in the polymer. By analogy with the distribution of the components of alcohol–water mixtures in simple ionic systems, it is thought that only an high co‐solvent concentration brings about an extensive and possible cooperative depletion of the clusters of firmly‐bound water molecules in the domain of the polylelectrolyte, favoring the transition to the α‐helical structure. On the other hand, CD spectral patterns show that the addition of NaCl in the alcohol‐rich–water mixtures of charged poly‐L‐lysine gives rise to a transition from the α‐helical to a β‐structures conversion obeys a first‐order rate law at all times, with a rate constant dependent on solvent composition and ionic strength. In these conditions, the rate of the process is close to that found for the thermally induced α–β transition. Higher polymer concentration and/or ionic strength cause a phase separation of β‐PLL, suggesting that in this case interchain reactions (where hydrogen bonding should play the major role) predominate. Titration experiments on charged α‐helical poly‐L‐lysine in 85% or 90% isopropanol mixtures confirm the occurrence of a conformational transition, which takes place within a degree of dissociation α of 0.2–0.75. The transition is accompanied by a visible turbidity, which increases as the titration proceeds. Implications of the solvent distribution around the macroion on the observed conformational phenomena are also discussed.
The effect of polydispersity on the nuclear magnetic resonancxce spectra of ply‐Y‐benzyl‐L‐glutamate
Authors: Milstien Julie B. , Ferretti James A. 
Published: May 2005

AbstractThe effect of poly dispersity on the nuclear magnetic resonance spectra of samples of poly‐γ‐benzyl‐L‐glutamateein the helix–random coil transition is studied. In the transitionregion the α‐CH proton resonance shows two peaks whose behavior does not change appreciably upon fractionation by gel permeation chromatography. Theoretical spectra were computed with both a polydispersity model of the transition and a model for slow nucleationof helix from completely random coil molecules. The results suggest that the double peak behavior in the nmr spectra results from a slow rate of helix nucleation rather than polydispersity.
Optical activity of simple peptides. I. Glycine oligopeptides with internal L‐alanyl or ‐L‐glutamyl residues
Authors: Lord Richard S. , Cox David J. 
Published: May 2005

AbstractOligopeptides containing glycine and one or two L‐alanyl or L‐glutamyl residues have been studied by circular dichroism (CD) and optical rotatory dispersion (ORD) in aqueous solution at pH 1.0, pH 6.0, and pH 10.0 and in aqueous ethanol. Two glycyl residues are required to remove effects of α‐carboxyl or amino titration on the optical activity of the internal alanyl or glutamyl residues. The CD spectra of the alanyl and protonated glutamyl residues are similar, having two regions of negative ellipticity around 215 nm resulting in a spectrum reassembling that of poly‐α‐L‐glutamic acid (PGA) at high pH. Another large positive band below 190 nm was observed for gly2‐glu2‐gly2 in water at pH 6 and 10 and for several peptides in aqueous ethanol. Residue ellipticities were approximately additive in every case except for peptides containing intrenal glutamyl residu at pH 6.0.
Induced optical activity in poly‐L‐lysine–methyl orange system
Authors: Hatano M. , Yoneyama M. , Sato Y. , Kawamura Y. 
Published: May 2005

AbstractThe absorption and cicular dichroism spectra of the complex of poly‐L‐lysine (PLL) in the random coil form with methyl orange (MO) have been measured in aqueous solution. A new absorption band is observed at the shorter wavelength compared with that of the free dye. Although MO does not show a formation of dimer or aggregation with an increase in concentration, circular dichroism bands are observed at the wavelength corresponding to the wavelength of the new absorption band. These induced circular dichroism bands may arise from the dimeric MO molecules bound to PLL in the random coil form. The main contribution to the interaction between MO molecules is shown to be the electro static interaction. The observed circular dichroism spectra and the configuration of dimeric MO molecules bound to PLL can be explained by the dipole couping mechanism.
On the electric polarization of DNA
Authors: Goswami D. N. , Gupta N. N. Das 
Published: May 2005

AbstractDielectric dispersion of DNA was studied in the frequency range 100 Hz–100 kHz at four different temperatures (6–30°C). The dielectric increment ε0–ε∞ increased with the rise of temperature. The relaxation time, on the other hand, decreased. Both the increase in dielectric increment and the decrease in relaxation time could not be explained on the basis of the counterion polarization theory. Dipole moment was estimated from Kirkwood theory. It was found to decrease systematically with temperature. Even at 0°C there was a dipole moment of 104D.
Random‐phase calculation of poly‐L‐proline II circular dichroism
Authors: Pysh E. S. 
Published: May 2005

AbstractRecent experiments have shown that the circular dichroism of poly‐L‐proline II is negative from 130 to 220 nm. Therefore, calculations based on exciton interactions alone cannot give the observed spectrum.The present calculations were carried out in the framework of the random‐phase approximation. It includes exciton coupling of π‐π* transitions. It also couples the π‐π* transitions to the higher energy density of states (1) of the polymer chain via atomic polarizabilities, and (2) of bound solvent molecules. The relative importance of (1) and (2) is discussed in light of available experimental evidence.Qualitatively, (1) and (2) modify the excition‐only results in the same way: the negative band near 200 nm shifts to longer wavelengths and increases in intensity; the crossover near 215 nm shifts to longer wavelengths; and the positive band near 225 nm shifts to longer wavelengths and decreases in intensity.
The structure of water absorbed in collagen. I. The dielectric properties
Authors: Hoeve C. A. J. , Lue P. C. 
Published: May 2005

AbstractThe dielectric constant and the loss factor of water in collagen are measured for various water, NaCl, and HCl contents at frequencies ranging from 102 to 105 Hz and at temperatures ranging from −70° to +23°C. For all measurements, both the dielectric constant and the loss decrease monotonically as the frequency increases, or the temperature decreases; the absence of a maximum in the loss curves as a function of temperature and frequency indicates an extremely broad spectrum of relaxation times. By shifting the curves obtained for the dielectric constant and the loss factor along the log–frequency axis, all data, obtained at different temperatures, can be represented on master curves valid for 23°C.In order to explain these results, water molecules are assumed to be hydrogen bonded to each other in long chains. All water molecules in a chain can, cooperatively, be oriented in two different directions along the channel, resulting in large, reversible, dipole moments. These chains are not rigid, but are flexible liquid‐like structures. Diffusion of chains as entities is assumed to be the rate‐limiting step for dipole reorientation. Although the rate of diffusion decreases inversely proportional to chain length, the activation energy is independent of chain length. At lower temperatures, diffusion becomes slower, until at the glass point, approximately −100°C, it ceases.
The influence of temperature variations and pressure treatment on proteins and DNA in the solid state
Authors: Rossiter V. 
Published: May 2005

AbstractLow‐frequency dielectric measurements have been made in the temperature range from −180°C to +110°C on DNA and a number of proteins in the solid state. The results suggest that a molecular rearrangement may occur in the temperature interval +60°C to +80°C. In terms of these measurements the transition appears to be reversible in DNA if the material remains at +20°C for longer than 60 hr. Such a time‐dependent recovery has not been observed for proteins. The application of a pressure of ∼150 MN m−2 for a 3‐min. period appears to be capable of reversing the thermal transition in at least some of the proteins studied. These results are compared with the results available from studies of the influence of temperature and pressure variations on similar biological materials in aqueous solutions.
A quantitative model of cooperative effects in aspartate transcarbamylase and related hybrid molecules
Authors: Diesendorf Mark 
Published: May 2005

AbstractThe hypothesis is made that cooperative (homotropic) effects in aspartate transcarbamylase (ATCase) and closely related hybrid molecules can be treated on the same basis, by expressing the effects in terms of cooperative interactions between catalytic sites. Then, provided the hybrid CnnnCsss[R] exhibits cooperativity experimentally, it is deduced that at least two parameters are required for a consistent description of cooperative effects in ATCase.On this basis, a quantitative model is proposed that has cooperative interactions of two types: (1) a cooperative interaction of strength U between a pair of native catalytic sites situated in different catalytic trimers, and joined by a regulatory dimer; (2) an indirect cooperative interaction Ū, between any pair of native catalytic sites in the same catalytic trimer, which is transmitted via two regulatory dimers. The model is consistent with the observation that the isolated catalytic trimer does not exhibit cooperativity, and that cooperative effects require the integrity of the regulatory dimers.In this model, the hybrid molecule CnnnCsss[R] becomes simply a one‐dimensional Ising model for three sites with pair interactions Ū, and the hybrid CnssCnss[R] becomes an Ising model for two sites with interaction U/3. The model of native ATCase is essentially two Ising systems (the catalytic subunits), each with three sites having intrasubunit pair interactions Ū, coupled together with three intersubunit pair interactions U.The parameters Ū and U can be determined by comparing the exact solutions for the saturation curves of the two Ising models with the curves obtained from cooperativity measurements on the corresponding hybrid molecules. The theory can be readily tested, when accurate experimental data become available, by substituting the values of Ū and U determined from the hybrids into the model of native ATCase, or into models of other hybrids.