bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of temperature and pH on the β–helix transition of poly(L‐lysine) in sodium dodecyl sulfate solution
Authors: Satake Iwao , Yang Jen Tsi 
Published: December 2004

AbstractThe conformational phase diagram of poly(L‐lysine) (4.6 × 10−4 M, residue) in sodium dodecyl sulfate (1.6 × 10−2 M) solution was constructed from circular dichroism results at various temperatures and pH's. Poly(L‐lysine)–sodium dodecyl sulfate complexes undergo a β–helix transition upon raising the pH of the solution. The transition pH tends to shift downward at elevated temperatures. No helix–β transition can be detected for poly(L‐lysine) in sodium dodecyl sulfate solution (pH > 11) even after 1‐hr heating at 70°C. This is in marked contrast with uncharged poly(L‐lysine) solution without sodium dodecyl sulfate, which is converted into the β‐form upon mild heating of the solution above 50°C.
Levans. V. Kinetics of the acid hydrolysis of Streptococcus salivarius levan
Authors: Lauren M. D. , Stivala S. S. , Bahary W. S. , Long L. W. 
Published: December 2004

AbstractThe kinetics of the acid hydrolysis of Streptococcus salivarius levan were studied by examining the weight‐average molecular weight. The molecular weights were obtained in a continuous manner from light scattering. Two first order reactions were observed: an initial rapid reaction in competition with a slower reaction.Activation energies, activation entropies, as well as the rate dependence upon substrate and hydrogen ion concentrations were determined. The data seem to indicate that the fast reaction is related to the breaking of branch‐point bonds while the slower reaction is related to the breaking of main‐chain bonds. Thus, levan hydrolysis seems to be fundamentally different from the completely random degradation of other branched polysaccharides, i.e., dextran, glycogen, and amylopectin.
Studies on interaction between poly(L‐lysine) and DNA of varied G + C contents
Authors: Li Hsueh Jei , Herlands Louis , Santella Regina , Epstein Paul 
Published: December 2004

AbstractInteraction between polylysine and DNA's of varied G + C contents was studied using thermal denaturation and circular dichroism (CD). For each complex there is one melting band at a lower temperature tm, corresponding to the helix–coil transition of free base pairs, and another band at a higher temperature t′m, corresponding to the transition of polylysine‐bound base pairs. For free base pairs, with natural DNA's and poly(dA‐dT) a linear relation is observed between the tm and the G + C content of the particular DNA used. This is not true with poly(dG)·poly(dC), which has a tm about 20°C lower than the extrapolated value for DNA of 100% G + C. For polylysine‐bound base pairs, a linear relation is also observed between the t′m and the G + C content of natural DNA's but neither poly(dA‐dT) nor poly(dG)·poly(dC) complexes follow this relationship. The dependence of melting temperature on composition, expressed as dtm/dXG·C, where XG·C is the fraction of G·C pairs, is 60°C for free base pairs and only 21°C for polylysine‐bound base pairs. This reduction in compositional dependence of Tm is similar to that observed for pure DNA in high ionic strength. Although the t′m of polylysine‐poly(dA‐dT) is 9°C lower than the extrapolated value for 0% G + C in EDTA buffer, it is independent of ionic strength in the medium and is equal to the tm0 extrapolated from the linear plot of tm against log Na+. There is also a noticeable similarity in the CD spectra of polylysine· and polyarginine·DNA complexes, except for complexes with poly(dA‐dT). The calculated CD spectrum of polylysine‐bound poly(dA‐dT) is substantially different from that of polyarginine‐bound poly(dA‐dT).
Optical Kerr effect in biopolymer solutions
Authors: Coles H. J. , Jennings B. R. 
Published: December 2004

AbstractThe electric field in a single mode, YAG laser beam has been used to induce orientational birefringence in solutions of tobacco rattle virus, DNA, heparin, and hyaluronic acid. Using this laser in its “fixed‐Q” mode, laser pulses were generated which persisted for up to 200 μsec in which the effective electric field vector rose to 5 kV cm−1. The birefringence amplitudes so produced had a quadratic dependence on the effective field strength and thus obeyed Kerr's law. From the birefringence decay rates, relaxation times were determined which, by comparison with the birefringence induced by pulsed static electric fields revealed the biopolymer orientational origins of the effects. This indicated how these experiments can lead to the evaluation of particle geometry, the electronic contribution to electrical polarizabilities, and the optical polarizability of biopolymers in solution.
Evidence from circular dichroism for the binding of hydrogen ions and calcium ions by poly(L‐proline)
Authors: Lo Jung‐Teh , Mattice Wayne L. 
Published: December 2004

AbstractThe positive circular dichroism band observed near 228 nm with poly(L‐proline) responds in a similar fashion to HCl and CaCl2. The spectra in the HCl solutions are compatible with a simple binding equation and a pK near −2 for the dissociation of a proton from a protonated peptide bond in poly(L‐proline). The data obtained in CaCl2 is susceptible to the same analysis, suggesting a pK near −1.5 for the dissociation of a calcium ion from its complex with poly(L‐proline).
The interaction of poly (N5‐(3‐hydroxypropyl)‐ L‐glutamine) with solvent components in water/dioxane mixtures
Authors: Inoue Hideo , Izumi Taro 
Published: December 2004

AbstractThe preferential binding of solvent components with a nonionic homopolypeptide, poly(N5‐(3‐hydroxypropyl)‐L‐glutamine), ([Gln((CH2)3OH)]n), has been determined in water/dioxane mixtures using differential refractometry. The degree of preferential binding was calculated from the difference between the refractive index increments of [Gln((CH2)3OH)]n obtained from experiments carried out under two conditions: experiments where the molality of dioxane was kept identical in both compartments of the differential cell, and experiments where the chemical potential was kept identical. The polypeptide was preferentially hydrated between 10 and 70 wt % of dioxane; the amount of preferential hydration per gram of the mixed solvent increases monotonically (with a plateau region between 40 and 60 wt %) with the dioxane concentration. A monotonic increase was also observed in the degree of helicity of the polypeptide.The absolute amounts of water and dioxane bound by [Gln((CH2)3OH)]n were investigated in the frozen state by the method of nuclear magnetic resonance. Hydration was measured using a mixed solvent, water/dioxane‐d8; dioxane solvation was measured using a mixed solvent, dioxane/D2O. The polypeptide binds about 0.35 g of water per g of the polymer in aqueous solution, and hydration decreases gradually with an increase in dioxane concentration. On the other hand, the amount of dioxane solvation increases to 0.04 g per g of the polymer in the dioxane concentration range between 0 and 20 wt %, and then levels off. The rapid increase in solvation is observed before the conformational transition from random coil to α‐helix occurs in [Gln((CH2)3OH)]n.The dependence of the preferential and absolute binding of solvent components to [Gln((CH2)3OH)]n on dioxane concentration and the conformational change in the homopolypeptide suggest that addition of dioxane to aqueous solutions induces lowering of water activity and that the helical structure of the polypeptide is enhanced by the formation of intrachain hydrogen bonds. The validity of the frozen method is also discussed.
Threshold effects observed in conformation changes induced by electric fields
Authors: Pörschke Dietmar 
Published: December 2004

AbstractSingle‐stranded polynucleotides are used as model systems for the investigation of conformational changes induced by electric fields. It is demonstrated that the single‐strand helix–coil transition in poly(A), poly(dA), and poly(C) can be induced by application of high electric fields. The transition is measured by UV absorbance using polarized light at an angle of 54.8° with respect to the vector of the electric field and by electrodichroism. A linear increase of the absorbance, reflecting the helix‐to‐coil transition, is observed at increasing field strength. When ions are added to the polymer, electric fields do not induce conformation changes, unless a threshold value of the electric field strength E0 is exceeded. At field strengths above this threshold, the degree of transition is a linear function of the increase in field strength. The threshold values E0 show a linear increase with the logarithm of the ion concentration. Bivalent ions cause thresholds at much lower ion concentrations than mo‐novalent ions. The shielding efficiency of ions is correlated to the binding affinity of these ions to the polymer.The conformation changes induced by the field and the existence of thresholds can be explained on the basis of dissociation field effects. Similar threshold effects may be expected for other macromolecules as well as for membrane structures and may be important in the regulation of bioelectricity.
Étude expérimentale de l'auto‐association des molécules modèles dipeptidiques. II. Association stéréosélective des molécules énantiomères
Authors: Cung Manh Thong , Marraud Michel , Neel Jean 
Published: December 2004

AbstractModes of aggregation fo alanine‐, norvaline‐ and valine‐contaiing dpepetides with the general formula R1C1O1N2H2CHR2C2O2N3H3R3 have been studied in CCl4 solution by using infrared and nuclear magnetic resonance spectroscopies. Solutions of the pure L isomer and of the racemic mixture do not give identical data. At a given concentration, the racemic mixtrue is more aggregated than the pure enantiomer, and the difference, negligible in the case of alanine derivative, increases wiht the bulkiness of the side cahin R2.The results show that a selective interaction takes place between enantiomeric molecules, resulting ina dimer associating tow inverse configurated C5 conformers. The stabilizaion of this dimer proceeds from two symmetrical and intermolecular H3 … O1 hydrogen bondings.
Ring‐current effects in the nmr of nucleic acids: A graphical approach
Authors: Giessner‐Prettre Claude , Pullman Bernard , Borer Philip N. , Kan Lou‐Sing , Ts'O Paul O. P. 
Published: December 2004

AbstractThe spatial dependence of the ring‐current magnetic anisotropy of nucleic acid bases is presented in a series of graphs in cylindrical coordinates. The curves may be used to calculate the ring‐current shift at a point in a cylinder of radius 10Å extending 8 Å above and below each ring of the base. These distance effects are found to influence considerably the predicted chemical shifts of nucleic acid protons, particularly in RNA duplexes. The contribution of polarization (electric field) effects and the diamagnetic anisotropy of individual atoms (local Δχ) are briefly discussed.
Co‐oligopeptides of aromatic amino acids and glycine with variable distance between the aromatic residues. VII. Enzymatic synthesis of N‐protected peptide amides
Authors: Saltman Robert , Vlach Dagmar , Luisi Pier Luigi 
Published: December 2004

AbstractSeveral N‐protected peptide amides, containing two aromatic residues spaced by one glycyl residue, have been enzymatically synthesized starting from P‐Ar‐OH and H‐Gly‐Ar‐NH2 (P is the protecting group and Ar is the aromatic residue) and using α‐chymotrypsin as the catalyst for the coupling step. Reactions have been carried out in water solution, at room temperature, and afford yields ranging between 20 and 75% ca. This coupling reaction occurs in a much more restricted set of conditions than the hydrolysis reaction, e.g., only within a small pH range (ca. 6.5–7.5) and with particular buffering agents. The advantages and limitations of this type of reaction, compared with conventional coupling procedures, are discussed.
Thermodynamics of mucopolysaccharide–dye binding. I. Identification of free and bound dye via membrane filtration: Acridine orange–dermatan sulfate system
Authors: West Seymour S. , Hurst Robert E. , Menter Julian M. 
Published: December 2004

AbstractStoichiometric mixtures of acridine orange with dermatan sulfate at total dye concentrations ⩽ 1 × 10−5 M show fluorescence maxima at 540 nm and 660 nm on excitation at 436 nm. By means of membrane filtration, it is directly demonstrated that the species emitting at 540 nm is due only to unbound dye whereas the 660‐nm emitting species is due to bound dye. It is, therefore, possible to differentiate unbound acridine orange from its dermatan sulfate complex solely by spectroscopic methods. Thermodynamic binding parameters can be calculated from rapid spectroscopic measurements without disturbing the system.
Theoretical conformational analysis on Cyclo(prolyl‐phenylalanyl) peptides
Authors: Ajò David , Granozzi Gaetano , Di Bello Carlo 
Published: December 2004

AbstractEmpirical energy calculations on cyclo(L‐Pro‐L‐Phe) and cyclo(L‐Pro‐D‐Phe) indicate that different conformations are possible for each molecule. The theoretical results are compared to ir, nmr, and crystallographic data. The interdependence between diketopiperazine ring and side‐chain conformations is also discussed.
Polynucleotide models. II. Prediction of the radial position and tilt of the bases from the helical parameters
Authors: Zimmerman Steven B. 
Published: December 2004

AbstractA simple geometrical analysis is applied to base‐stacking interactions in helical polynucleotides. A base‐pair or other H‐bonded arrangement of bases is represented by a corresponding plane. In a helical structure, these planes will intersect each other if the bases are not perpendicular to the helix axis. The tilt of the bases and the position of intersection of these planes are geometrically related, and demonstrate the interrelation of the tilt of the bases with their radial position. This approach may be coupled with a constraint which predicts the radial position of the bases based solely upon the helical parameters. These two constraints taken together allow a simple means to predict the approximate position and tilt of a given H‐bonded arrangement of bases placed according to specified helical parameters. For a number of polydeoxyribonucleotides, there is more than one base position and tilt consistent with these constraints, while there is only one base position and tilt indicated for each of the polyribonucleotides examined.
Raman spectral studies of nucleic acids. XVI. Structures of polyribocytidylic acid in aqueous solution
Authors: Chou C. H. , Thomas G. J. 
Published: December 2004

AbstractRaman spectra of polyribocytidylic acid show the formation of an ordered single‐stranded structure [poly(rC)] at neutral pH and an ordered double‐stranded structure containing hemiprotonated bases [poly(rC)·poly(rC+)] in the range 5.5 > pH > 3.7. Below 40°C, poly(rC) contains stacked bases and a backbone geometry of the A‐type, both of which are gradually eliminated by increasing the temperature to 90°C. Below 80°C, poly(rC)·poly(rC+) contains bases which are hydrogen bonded and stacked and a backbone geometry also of the A‐type. In this structure the bases of each strand are shown to be structurally identical, i.e., hemiprotonated, and therefore distinct from both neutral and protonated cytosines. Infrared and Raman spectra indicate the existence of a center of symmetry with respect to the paired cytosine residues, which suggests that the additional proton per base pair is shared equally by the two hydrogen‐bonded bases. Denaturation of poly(rC)·poly(rC+) occurs cooperatively (tm ≈ 80°C) with elimination of base stacking, base pairing, and the A‐helix geometry. Each of the separated strands of the denatured complex is shown to contain comparable amounts of both neutral and protonated cytosines, most likely in alternating sequence [poly(rC, rC+)]. In both poly(rC, rC+) and poly(rC), at 90°C, the backbones do not exhibit the phosphodiester Raman frequencies characteristic of other disordered polyribonucleotide chains. This is interpreted to mean that the single strands, though devoid of base stacking and A‐type structure, contain uniformly ordered backbones of a specific type. Fully protonated poly(rC+), on the other hand, forms no ordered structure and may be characterized as a disordered (random chain) polynucleotide at all temperatures. Several Raman lines of poly(rC) are absent from the spectrum of poly(rC)·poly(rC+) and vice versa. These frequencies, assigned mainly to vibrations of the ribose groups, suggest that the furanose ring conformations are different in the single‐stranded and double‐stranded structures of polyribocytidylic acid. Several other Raman group frequencies have been identified and correlated with the polymer secondary structures.
Reduction of ferriprotoporphyrin IX to the ferroderivative by copoly(4‐vinylpyridine‐N‐(p‐vinylbenzyl)‐3‐carbamoyl‐1,4‐dihydropyridine) in dimethyl sulfoxide
Authors: Tsuchida Eishun , Hasegawa Etsuo 
Published: December 2004

AbstractThe copolymer which has both ligand sites (4‐vinylpyridine) and redox sites (N‐(p‐vinylbenzyl)‐3‐carbamoyl‐1,4‐dihydropyridine) was synthesized by the dithionite reduction of the copoly(4‐vinylpyridine‐N‐(p‐vinylbenzyl)‐3‐carbamoylpyridinium chloride) and the reduction of a central ferric‐iron of ferriprotoporphyrin IX by the above‐described copolymer was studied spectrophotometrically in dimethyl sulfoxide. The rate of the reduction by the copolymer was much faster than by N‐benzyl‐3‐carbamoyl‐1,4‐dihydropyridine. This acceleration by the copolymer could be explained by the intramolecular reduction of ferriprotoporphyrin IX which was coordinated by the pyridine residue of the copolymer.
Determination of the rates and barriers to conformational isomerization in the dipeptide L‐pro‐L‐4hyp by direct 13C nmr thermal equilibration
Authors: Roques B. P. , Garbay‐Jaureguiberry C. , Combrisson S. , Oberlin R. 
Published: December 2004

AbstractThe 13C nmr equilibration method lends itself as a tool for study of conformational rate processes involving aqueous media in conjunction with high activation barriers. This method is applied for measurement of kinetic and thermodynamic parameters of isomerism in the dipeptide L‐Pro‐L‐4Hyp. The activation barrier for cis ⇋ trans interconversion (ω 0° → 180°) is determined, ΔG≠ = 22.3 kcal/mol. From low‐temperature study, an upper limit ΔG≠ < 9.7 kcal/mol is evaluated for cis′ ⇋ trans′ rotation (ψ −40° → 160°). These data are compared with computed values found in literature. The results are discussed in connection with the helix–coil transition of collagen involving Gly‐L‐Pro‐L‐4Hyp as nucleation sites.
Comparative fluorescence studies of native and crosslinked glucose oxidase
Authors: Solomon Beca , Shinitzky Meir 
Published: December 2004

AbstractThe binding characteristics of flavin adenine dinucleotide (FAD) to apoenzyme preparations obtained from native and intramolecularly crosslinked glucose oxidase were determined and compared. The dissociation constants Kdiss as well as rates of recombination of FAD with the two apoenzyme preparations, were independently evaluated from fluorescence quenching of either the tryptophans of FAD. The Kdiss values thus obtained were <10−19M for native glucose oxidase and 4 ± 1 × 10−7M for the crosslinked enzyme. The recombination of apo glucose oxidase with FAD, which is presumably diffusion controlled, is followed by an apparent first order decrease in fluorescence intensity of both the protein tryptophans and FAD, with a rate constant around 0.2 min−1. This could be related to conformational changes which occur immediately after binding of FAD to the apoenzyme, an interpretation which is supported by the markedly different results obtained in the analogous experiments with the crosslinked enzyme. A model for the conformational characteristics of glucose oxidase, based on this study, is proposed.
The temperature‐induced conformational transition of immobilized chymotrypsinogen
Authors: Brynda E. , Bleha M. 
Published: December 2004

AbstractA method has been suggested for obtaining kinetic thermodynamic data on conformational transitions of insoluble proteins by fluorescence measurements. The method was used for treatment of the temperature‐induced conformational transition of chymotrypsinogen bonded to the hydroxyethyl methacrylate Spheron matrix. The bonding to Spheron causes destabilization of the native conformation of chymotrypsinogen. Two types of transition of immobilized chymotrypsinogen have been found which are controlled by first‐order kinetics with different rate constants. The entropy and enthalpy changes were smaller than for free chymotrypsinogen in solution. The data obtained are interpreted as an effect of the physical interaction of the protein in the activated and denatured states with the polymeric matrix.
Influence of temperature and ionic strength on the low‐frequency dielectric dispersion of DNA solutions
Authors: Tung Ming Sung , Molinari Robert J. , Cole Robert H. , Gibbs Julian H. 
Published: December 2004

AbstractThe dielectric properties of DNA solutions at low frequencies (5 Hz to 2 kHz) have been measured by means of a four‐terminal bridge method utilized to minimize electrode polarization errors. At 24°C native salt‐free DNA has a very large specific dielectric increment, Δε/c = 9.8 × 106 l/mol and a very low frequency relaxation centered at 18 Hz. Both the dielectric increment and the relaxation time are greatly decreased by partial heat denaturation at temperatures above 60°C or by addition of salt, the effects being much larger for divalent anions. These results are shown to be in qualitative agreement with theoretical treatments of counterion fluctuation polarization by McTague and Gibbs for the equilibrium case and by Mandel for relaxation. The ratio of the relaxation time for the low‐frequency process to that previously observed at much higher frequencies suggests that these relaxations result from counterion fluctuations along the longitudinal and transverse axes of the molecule, respectively.
Block oligopeptides (L‐lysyl)m‐(L‐alanyl)L‐tyrosyl‐(L‐alanyl)n‐ (L‐lysyl)m. I. Synthesis through fragment condensation and characterization
Authors: Mayer R. , Caille A. , Spach G. 
Published: December 2004

AbstractModel peptides containing one aromatic residue were synthesized and characterized in order to investigate their interactions with polynucleotides. Chromatographically pure block oligopeptides (L‐alysyl)m‐(L‐alanyl)n‐ L‐tyrosyl‐ (L‐alanyl)n, with n = 3 and m=3 or 6, were prepared by fragments condensation using the mixed anhydride method. The protected fragments were prepared by stepwise addition of amino acid residues through the dicyclohexylcarbodiimide method. The purity of the intermediate coupling product was analyzed by gradient elution chromotography on carboxylmethylcellulose. Both block oligopeptides were isolated by preparative chromatography on carboxymethylcellulose. The different features of these syntheses are discussed.
Measurement of the expected DNA lengthening caused by mono‐ and bisintercalating drugs using electron microscopy
Authors: Butour J. L. , Delain E. , Coulaud D. , Le Pecq J. B. , Barbet J. , Roques B. P. 
Published: December 2004

AbstractPM2 DNA molecules were treated with intercalating reagents (ethidium bromide, ethidium dimer, acridine dimer) and observed by electron microscopy. The adaptation of different electron microscopy techniques has enabled the determination of DNA lengthening upon drug intercalation. A 50% length increase was generally obtained for DNA saturated with the drugs. This result is in agreement with the intercalation model proposed by Lerman. In some cases (ethidium dimer), an increase of length larger than 50% can be obtained. Experimental conditions of DNA spreading strongly interfere with the DNA–drug interaction. In some cases it was possible to estimate the apparent binding constants and also to distinguish the mono‐ from the bisintercalating derivatives in their reaction with DNA.