bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational studies of linear β‐D‐1,4′‐mannan and galactan
Authors: Sundararajan P. R. , Rao V. S. R. 
Published: December 2004

AbstractThe nonbonded interaction energy of disaccharides, mannobiose and galactobiose and polysaccharides mannan and galactan have been computed as a function of dihedral angles (ϕ,ψ). The conformation (40°, −20°) has been preferred for the mannan chain from nonbonded interaction energy considerations. The O5…O3′ type of intramolecular hydrogen bond has been found to be possible in the above conformation. Comparison of the allowed region of mannan with those of cellulose and xylan indicates that the monomer unit, in mannan chain has slightly higher freedom of rotation than that of cellulose and less than that of xylan. As in cellulose and mannan, the freedom of rotation of the monomer units in β‐1,4′ galactan is highly restricted. Unlike mannan (which prefers an extended conformation) the β‐1,4′ galactan prefers a helical conformation similar to amylose. Just as in amylose the O2…O3′ type hydrogen bond between contiguous residues is also possible in β‐1,4′ galactan.
Conformational and kinetic studies of synthetic polypeptides by NMR
Authors: Warashina Akira , Iio Takayoshi , Isemura Toshizo 
Published: December 2004

AbstractThe α‐helix–coil transition of poly‐L‐leucine, poly‐L‐alanine and poly‐L‐methionine in chloroform–trifluoroacetic acid system was studied by nuclear magnetic resonance (NMR) and optical rotatory dispersion (ORD). The kinetics of the hydrogen–deuterium exchange in the peptide was also followed in these polymers by means of NMR. Two types of the NMR spectra and the hydrogen–deuterium exchange reaction were found, corresponding to the high and low molecular weight polypeptides. In high molecular weights, the NH and α‐CH resonance lines gave single peaks and the hydrogen–deuterium exchange was expressed as a single first order reaction. In low molecular weights, the NH and α‐CH lines were separated into two peaks, corresponding to helical and random‐coiled states, respectively, and the exchange react ion was expressed as super‐position of a very rapid exchange reaction in the random‐coiled part and another slow exchange reaction of the first order in the helical part. These results suggest that the helix–coil interconversion of low molecular weight polypeptides has a longer relaxation time (⩾ 4.5 × 10−3 sec) than that of high molecular weight polypeptides.
Critical comparison of the experimental optical activity of helical polypeptides and the predictions of the molecular exciton model
Authors: Cassim Joseph Y. , Yang Jen Tsi 
Published: December 2004

AbstractThe predictions of the presently accepted molecular exciton model for the optical activity of helical polypeptides are in reasonable agreement with experimental spectra in the accessible wavelength range. However, crucial verification requires the detect of a significant negative rotatory hand just below the accessible range. A computer‐oriented method is utilized to obtain information concerning the inaccessible range. Optical rotatory dispersion computed by evaluation of the Kronig‐Kramers integral transform from the experimentally determined circular dichroism of several helical homopolypeptides in solution are compared with the experimentally determined optical rotatory dispersion. Computed and experimental curves are congruent within an uncertainty approaching that of the experimental technique, whatever the polypeptide sample lot, side chains, and solvent. It is shown that t his agreement is not a computational or experimental artifact. These results can be interpreted in two ways: (1) that the predicted band does not exist, and (2) that the perturbation of the predicted band is being negated by other inaccessible bands in the vacuum ultraviolet. Arguments are presented to show that the first of these two possibilities is more probable.
Instability in pressure‐dependent sedimentation of monomer—polymer systems
Authors: Johnson Michael , Yphantis David A. , Weiss George H. 
Published: December 2004

AbstractThe possibility of convection in velocity sedimentation studies on pressure dependent associating systems is known both experimentally and theoretically. We present accurate numerical solutions to the Lamm equation to illustrate this phenomenon for monomer–polymer systems. An approximate theory based on the absence of diffusion is then developed to predict the onset of convection. Comparison of the theory with the numerical solutions shows it to be quite accurate.
A rapid method for the preparation of amino acid resin esters for merrifield solid‐phase peptide synthesis
Authors: Monahan Michael W. , Gilon Chaim 
Published: December 2004

AbstractAn improved method for the preparation of Merrifield resin esters is presented. This method is rapid, is free of racemization, and is not complicated by a quaternization side reaction. Chloromethylated resin beads, t‐butoxycarbonyl amino acid, and potassium t‐butoxide are heated at 80 °C in dimethylsulfoxide for one‐half hour to yield resin esters of suitable substitution for solid‐phase petide synthesis. All twenty of the BOC protected common amino acids were esterified to the resin by this method. Resin substitution values lie in the range of 0.13 meq/g (BOC‐Glu (NH2)) to 0.66 meq/g (BOC/Pro), with most of the amino acids yielding 0.3–0.4 meq/g (on a resin containing 0.8 meq Cl/g).
Effect of temperature on the induced cotton effects of acid polysaccharide–basic dye complexes
Authors: Nakajima Kazuko , Matsumura Go 
Published: December 2004

AbstractThe induced Cotton effect of some acid polysaccharide–thiazine dye complexes were studied at various temperatures. When the equivalent ratio of the anionic site of the polymer to the cationic dye was near unity, all the complexes examined showed remarkable Cotton effects corresponding to their absorption bands in the visible and ultraviolet regions, at neutral pH and room temperature. Although the structure of the hyaluronate complex resembles the carbohydrate backbone, the sign of the Cotton effects was opposite that of chondroitin sulfate complexes.When the temperature was raised, the hyaluronate–toluidine blue complex decreased the metachromatic shift in the absorption spectrum gradually; the amplitude of the Cotton effects of this complex decreased also. With a polysaccharide which has a carboxylate group as its only anionic site (such as carboxymethylcellulose or pectic acid), a similar effect of temperature was observed on its induced Cotton effects.With the chondroitin 4‐sulfate–toluidine blue complex, some reverse of the metachromatic shift was observed at higher temperature. However, the amplitude of its Cotton effects decreased up to 70 °C, then the sign of the effects reversed and the amplitude subsequently increased. A similar inversion of the sign of the Cotton effects was found with the chondroitin 6‐sulfate–toluidine blue complex, but at a lower temperature (about 40 °C).Charonin sulfate, a highly sulfated cellulose‐like glucan from a marine mollusca, showed a marked metachromatic effect on methylene blue even at the elevated temperature. The induced Cotton effects of this complex were also affected by temperature and the inversion of the sign was observed.When the pH was lowered, the amplitude of the Cotton effects of the hyaluronate‐toluidine blue complex decreased and diminished at pH 3, at room temperature. With chondroitin 4‐sulfate, the induced Cotton effects were remarkable at such a low pH; however, the amplitude of the effects decreased with elevated temperature and no inversion was observed. The optical rotatory dispersion of the chondroitin 6‐sulfate–toluidine blue complex was reversed by acidifying to pH 3, and the amplitude of the Cotton effects decreased by elevating the temperature.
Conformational aspect of polypeptide structure. XLIV. Conformational transitions of poly(N‐methyl‐alanines) induced by trifluoroacetic acid
Authors: Goodman Murray , Chen Fu , Prince Frank R. 
Published: December 2004

AbstractThe synthesis of poly(N‐methyl‐L‐alanine) and poly (N‐methyl‐DL‐alanine) are described. The polymers were examined by 220 MHz high‐resolution nuclear magnetic resonance (nmr) and circular dichroism (CD). The results demonstrate that poly(N‐methyl‐L‐alanine) exists as an ordered helical structure with all the amide bonds in the trans configuration in appropriate solvents. As trifluoroacetic acid (TFA) is added to the solutions of the polymer in helix‐supporting solvents, resonances corresponding to both trans and cis amide conformations of N‐methyl, C‐methyl, and α‐CH are observed. The presence of both the trans and the cis peptide bonds in a polymer chain disrupts the ordered structures. Our conclusions from CD data are in agreement with the nmr results. Ultracentrifugation shows that degradation of the polymer chain does not occur during the TFA treatment.
Kinetic study on unzippering of polynucleotides and order–order transition in polypeptides
Authors: Chay Teresa Ree , Stevens Charles L. 
Published: December 2004

AbstractSolutions are presented for N + 1 sequential and reversible first‐order reactions for which the magnitude of the reverse rate constant, kb, for all steps except the last is identical. Also the magnitude of the forward rate constant, kf, for all steps except the first and last is identical. The initial and final steps are nucleation reactions; therefore, the initial and final kf are modified by the factors σ′ and γ respectively. The final kb is modified by the factor γ σ. The ratio kb/kf is defined as s, which has the same meaning as s in the Zimm‐Bragg theory. The mathematical model is intended to apply to polymeric molecules of N segments and allows the calculation of the mole fraction of molecules in state i at any time t, Ci(t). A molecule in state i has i unreacted segments and N – i reacted ones. Because the reactions are sequential, all reacted segments are contiguous. Our numerical results show that when σ′ is much less than unity and the forward reaction is favored, the relaxation curve is sigmoidal. If, however, the forward and reverse reactions are equally favored (i.e., s ≃ 1) the relaxation curve is a straight line. When s and σ′ are near unity, the curve is exponential for a considerably large fraction of the reaction. Further, in the exponential for a considerably large fraction of the reaction. Further, in the exponential phase of the reaction, the relaxation time is proportional to N2 for highly cooperative systems (i.e., Nσ ≪ 1). As found by Pipkin and Gibbs, if N is sufficiently large and s is less than unity (e.g., N ≳ 50 and s ≃0.9) the relaxation curve is largely linear with a slope inversely proportional to N. Applications are given for the unwinding of double‐helical poly(A·U) and the order–order transition in poly‐L‐proline.
Dielectric properties of polyelectrolytes. V. Dielectric dispersion of heavy meromyosin
Authors: Minakata Akira , Kobayashi Shoyu 
Published: December 2004

AbstractDielectric constant and dielectric loss of heavy meromyosin (HMM) were measured with varying pH. HMM showed a broader dispersion pattern than that with a single relaxation time especially on the high‐frequencey side. The dielectric increment increased sharply with pH, above pH 6, whereas the mean relaxation time and whole dispersion pattern were unchanged in the same region. The values of the increment and the mean relaxation time were much larger than those of usual globular proteins. The dispersion profile, pH dependence, and values of the increment are well explained by Oosawa's counterion fluctuation theory. Other mechanisms are more or less inadequate to our results. In the low pH region below the isoelectric precipitation region, both the increment and the mean relaxation time decreased; this is probably due to partial denaturation and suppression of the dissociation of carboxyl groups. An experiment on a urea‐denatured sample supports this assumption. The biological significance of the pH dependence is discussed.
Rigidity of α‐helical polypeptides. A new method of obtaining the persistence length from viscosimetric data
Authors: Morcellet M. , Loucheux C. 
Published: December 2004

AbstractThe hydrodynamic properties of α‐helical poly(L‐glutamic acid), (Glu)n in aqueous solutions and in mixtures of water with organic solvents have been interpreted in terms of the persistence length of the macromolecule. A modification of the method of Vitovskaya and Tsvetkov has been proposed in order to allow a more accurate determination of this parameter. The addition of an organic solvent increases strongly the rigidity of the helical conformation of (Glu)n. A comparison is made with some data of the literature of poly[N5‐(3‐hydroxy propyl)L‐glutamine], [Gln(CH2)3OH]n, and poly(γ‐benzyl‐L‐glutamate), [Glu(OBzl)]n.
Packaging of DNA in bacteriophage Heads: Some considerations on energetics
Authors: Riemer Steven C. , Bloomfield Victor A. 
Published: December 2004

AbstractWe have made quantitative estimates of some of the energetic factors to be considered in packaging of double‐stranded DNA in virus particles. Numerical calculations were made using parameters appropriate for T4 bacteriophage. The unfavorable factors, and the Gibbs free energies per mole virus at 20°C associated with them, are bending, 1.5 × 103 kcal/mol; conformational restriction upon condensation, 5.1 × 102 kcal/mol; polyelectrolyte repulsion, 2.1 × 105kcal/mol; and melting or kinking, 6.9 × 103 kcal/mol. These must be counterbalanced in the assembled phage by noncovalent bonding interactions between protein subunits in the phage‐head shell; by interactions between the DNA and polyvalent cations, especially putrescine and spermidine; nad perhaps by repulsive excluded volume and electrostatic interaction between the DNA and acidic polypeptides. Indeed, a rough estimate of the standard free energey of interaction between T4 DNA and the putrescine and spermidine contained in the head is ‐‐2.1 × 105 kcal/mol. In the absence of the other two sources of stabilization, each head protein subunit must contribute about 210 kcal/mol of binding energy.
Proton transfer in and polarizability of hydrogen bonds coupled with conformational changes in proteins. II. IR investigation of polyhistidine with various carboxylic acids
Authors: Lindemann Rainald , Zundel George 
Published: December 2004

AbstractPolyhistidine‐carboxylic acid systems are studied by ir spectroscopy. It is shown that OH ⃛N ⇌ O−…H+N bonds formed between carboxylic groups and histidine residues are easily polarizable proton‐transfer hydrogen bonds when the pKaof the protonated histidine residues is about 2.8 units larger than that of the carboxylic groups. From these results it bis concluded that OH ⃛N ⇌ O−⃛H+N bonds between glutamic or aspartic acid histidine residues in proteins may be easily polarizable proton‐transfer bonds. Furthermore, it is demonstrated that water molecules shift the proton‐transfer equilibria in these hydrogen bonds in favor of the polar structure, i.e., due to water or polar environments OH ⃛N ⇌ O−⃛H+N bonds with smaller ΔpKavalues become easily polarizable proton‐transfer hydrogen bonds. A consideration of the amide bands of polyhistidine shows that it can be present in five different conformations. It is shown that these conformational changes are strongly related to the degree of proton transfer. Hence, the degree of proton transfer, the degree of hydration, and conformation are not independent of each other, but are strongly coupled. Further proof for the interdependence of proton transfer and conformational changes are hysteresis effects, which are observed with studies of polyhistidine dependent on carboxylic acid, adsorption and desorption. OH ⃛N ⇌ O−⃛H+N bonds between aspartic and glutamic acid and histidine residues are present in hemoglobin, in ribonucleases, and in proteases, whereby this type of bond is preferentially found in the active centers of these enzymes. It is pointed out that hydrogen bonds with such interaction properties should be of great significance for structure and especially functions of proteins in which they are present.
Interaction of polyadenylic acid with methylated xanthines
Authors: Davies R. J. H. , Davidson N. 
Published: December 2004

AbstractPolyadenylic acid forms both 1 : 1 and 2 : 1 complexes with 3‐methylxanthine under appropriate conditions. While the binding isotherms for formation of these complexes are typical of strongly cooperative processes, their melting profiles are anomalous and indicate that intermediate species are present during the thermal dissociation process. Theobromine and theophylline do not form complexes with polyadenylic acid under similar conditions, and they do not hydrogen‐bond very strongly with 9‐ethyludenine in chloroform solution.
Physical behavior of gelatin gels: A simple model for connective tissue
Authors: Preston B. N. , Meyer F. A. 
Published: December 2004

AbstractThe swelling behavior of gelatin gels when immersed in buffer or in osmotically active solutions of dextran 500 has been studied, and the results can be described by means of the Flory‐Rehner theory of the thermodynamic properties of three‐dimensional network structures. The density of crosslinkages formed in the gel is found to be related to the concentration of gelatin at which gelation occurs. Values of rigidity moduli are estimated from the density of crosslinkages by use of the statistical thermodynamic theory of rubber elasticity. These values are in excellent agreement with direct measurements.
Effects of temperature on the polymerization of γ‐ethyl DL‐glutamate N‐carboxy anhydride in DMF initiated by tri‐n‐propylamine
Authors: Terbojevich M. , Cosani A. , Peggion E. , Scoffone E. 
Published: December 2004

AbstractPolymerization of γ‐ethyl DL‐glutamate N‐carboxy anhydride (NCA) in DMF has been carried out at various temperatures and with the use of tri‐n‐propylamine as the initiator. It was found that on decreasing the polymerization temperature the reaction rate is lowered but the molecular weight and the helix content of the final polymer are enhanced. An overall activation energy of ∼4 kcal/mole has been found for the polymerization process. Preliminary experiments carried out on the polymerization of γ‐benzyl D‐glutamate NCA in DMF and with tri‐n‐propylamine as the initiator showed a strong depressing effect of the CO2 evolved during the polymerization, both on the reaction rate and on the molecular weight of the polymer. All data are interpreted in terms of the Bamford‐Swarc mechanism.
Hétérogénéité des Sites de Fixation de la Proflavine sur le DNA
Authors: Bidet R. , Chambron J. , Weill G. 
Published: December 2004

AbstractThe desorption and melting with temperature of proflavine–DNA complexes has been studied by spectrophotometry and spectrofluorometry. Two methods are described to determine at each temperature the concentration of free and bound dye. The first one is based on the quenching of fluorescence of the free dye by the iodine ion, the second on fluorescence polarization measurements. It is shown that the sites where the bound dye fluoresces are thermally less stable than those where it is quenched, in such a way that a redistribution of the dye between the two types of sites occurs at intermediate temperatures, leading to a drop in the total fluorescence. This confirms the nature of the “emitting” sites which correspond to AT‐rich region, while “quenched” sites correspond to GC‐rich region. The first have a larger binding constant at room temperature, but only the latter are stabilized by dye intercalation. The desorption and melting have also been followed through the relative changes of absorption. The curves obtained at different wavelengths are not superimposed which is at variance with what is observed with complexes of proflavine with poly dAT and poly dG.dC. The beginning of the desorption process corresponds to minor variations at 445 nm, the maximum of absorption of the free dye, but large changes occur at 460 nm, the maximum of the difference spectrum of the complexes proflavine–poly dAT and proflavine‐poly dG.dC. The spreading of the melting curves for different wave lengths must therefore reflect the dependence of the absorption spectra of the dye on the nature of the neighboring bases. However, the action spectrum of the fluorescence, which gives the absorption spectrum of the “emitting” sites only, is identical with the total absorption spectrum of the bound dye.
Conformation of amylose in aqueous solution: Optical rotatory dispersion and circular dichroism of amylose–iodine complexes and dependence on chain length of retrogradation of amylose
Authors: Pfannemüller B. , Mayerhöfer H. , Schulz R. C. 
Published: December 2004

AbstractThe dependence on chain length of two characteristic properties of amylose, i.e., retrogradation and complex formation with iodine, have been studied by using enzymatically synthesized, homodisperse amyloses. The association rates of amyloses in water containing 5% dimethyl sulfoxide have a sharp maximum at a degree of polymerization P̄n of 80; shorter and longer molecules are much more soluble. The iodine complexes of amylose exhibit a strong Cotton effect in the range of the long‐wave absorption maximum (position depending on chain length) and two weaker Cotton effects at 480 and 350 nm. The long‐wave Cotton effect is most intense at about P̄n 50 and decreases rapidly for shorter and longer chains. This behavior is unexpected and is not in accordance with the further increase of λmax and λmax. The experiments can best be interpreted by assuming well ordered, stiff chains in the low molecular weight range (P̄n 50–80). For longer chains, the findings are discussed in the light of current concepts of amylose conformation in aqueous solution, namely the model of the broken helical chain (alternating stiff helical segments and unordered regions) and the model of a flexible coil without a significant helical content. However, according to the results given in this paper, a wormlike helical chain seems to be the most adequate model for amylose conformation in neutral solution.
Molecular weights and hydrodynamic properties for homogeneous native DNA, derived from diffusion, sedimentation, and viscosity measurements on polydisperse samples
Authors: Reinert K. E. , Strassburger J. , Triebel H. 
Published: December 2004

AbstractThe diffusion, sedimentation, and viscosity behavior of native DNA has been studied as a function of molecular weight absolutely determined by diffusion and sedimentation measurements between 106 and 20 × 106 Daltons. Only data for monodisperse subfractions of the polydisperse DNA samples investigated have been compared. They were derived by means of calculations based on individual sedimentation constant distribution and polymer parameters. The inconstancy of these parameters for the semi‐rigid DNA molecules over the range of different sub‐fractions of the polydisperse samples has been taken into account. A detailed description of the corresponding mathematical background as well as of the diffusion measurements has been given in the two preceding papers. For the homologous series of monodisperse native DNA molecules, three‐parameter equations have been determined representing the s0–[η], s0–M, and [η]–M relations as well as the D0–s0 and D0–M interdependence over the entire molecular weight range of interest. Furthermore a simple equation is given describing the molecular weight dependence of the Mandelkern‐Flory‐Scheraga parameter β in terms of s0 and [η]. The asymptotic value β∞ has been determined, primarily by measurements at finite molecular weights, to be 2.39 × 106, resulting in β values near 2.50 × 106 at M = 108 Daltons. The hydrodynamic properties of our two calf thymus DNA samples of highest molecular weight proved to be influenced by residual protein interactions resulting in a more compact conformation. Further data are given demonstrating the influence of the individual polydispersity of the investigated samples on diffusion constant and molecular weight averages.