bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dielectric changes in hyaluronate solutions at microwave frequencies as a function of concentration, system pH, and temperature
Authors: Jani S. K. , Dahiya J. N. , Roberts J. A. 
Published: December 2004

AbstractThe dielectric response of human umbilical cord hyaluronic acid in various environments has been studied at microwave frquencies using a resonant microwave cavity as a probe. Both the real and imaginary parts of complex dielectric constant and the loss tangent for hyaluronate solutions are obtained by utilizing equations for perturbation of a resonant cavity. Dielectric changes at room temperature have been observed in aqueous solutions of hyaluronic acid as a function of concentration ranging from 0 to 350 mg/ml. The data indicate the existence of ordered phases in hyaluronate solutions at selective concentrations, that is, exhibiting lyotropic‐type transitions. Hyaluronate solutions at 1.5 and 3 mg/ml concentrations have been studied at various pH in the range of 6–8 and at constant ionic strength 0.1. A temperature‐dependent transition in hyaluronate solution of 120 mg/ml concentration has been observed at physiological temperature. It is shown that this temperature‐dependent behavior can be related to the orientational polarizability term in the Debye theory of polar molecules in liquids.
Experimental support for a right‐handed vertical double helix
Authors: Mitra C. K. , Dhingra M. M. , Sarma Ramaswamy H. 
Published: December 2004

AbstractThe experimentally observed geometry of a miniature double helix of high anti (χCN fixed ≃ 120°) nucleic acid structure indicates substantial interstrand base stacking with little intrastrand base stacking. This geometry is consistent with the right‐handed vertical double helix in which the base planes are parallel to helical axis proposed by Olson [(1977) Proc. Natl. Acad. Sci. USA 74, 1775] from theoretical calculations. The experimental data do not agree with the left‐handed model in which the base planes are perpendicular to helical axis that has been proposed by Yathindra and Sundaralingam [(1976) Nucl. Acids Res. 3, 729]. The theoretically computed chemical shift changes for the various double‐helical configurations show that for the system examined, only the vertical model can explain the experimentally observed shift trends. The melting curve for the helix–coil transition for high anti dinucleoside monophosphate has been observed for the first time. Even though the experimental data support vertical double helices when χCN is fixed at 120°, data on naturally occurring nucleic acid structures indicate that they have no proclivity to enter into vertically stabilized double‐helical arrays.
Models for boundary effects on molecular rotation in membranes
Authors: Andersen Gregory R. , Mazo Robert M. 
Published: December 2004

AbstractRotational and wobbling diffusion coefficients for spherical and long‐chain molecules in membranes are calculated using a simple hydrodynamic model. Estimates of the contributions to the diffusion coefficients arising from hydrodynamic interactions between molecules and membrane interfaces are obtained and found to be small. For molecules containing polar head groups, we show that the presence of a membrane interface can produce a significant reduction in the wobbling diffusion coefficient over what would be obtained in an isotropic fluid.
Infrared study of the secondary structure of lac repressor and its tryptic core
Authors: Schnarr Manfred , Maurizot Jean‐Claude 
Published: December 2004

AbstractThe lac repressor and its tryptic core were studied by ir spectroscopy, and their β‐structure content was determined by analysis of the spectra. Using protein‐derived reference spectra, we find a β‐content for lac repressor of 18% and of 23% for its tryptic core. The higher amount of β‐conformation in the tryptic core is confirmed by another type of analysis (decomposition of the spectra in Gaussian curves). These results are discussed with respect to their implications for the structure of the N‐terminal “headpiece” of lac repressor and for the mode of interaction of lac repressor with lac operator.
Interaction of poly(α‐L‐glutamic acid) and sodium poly(α‐L‐glutamate) with solvent components in water–2‐chloroethanol mixtures
Authors: Morcellet M. , Loucheux C. 
Published: December 2004

AbstractThe preferential interaction of sodium poly(α‐L‐glutamate) and poly(α‐L‐glutamic acid) with the solvent components in water/2‐chloroethanol mixtures has been determined using density‐increment measurements. The degree of preferential interaction was deduced from the density increments at constant molality of 2‐chloroethanol and at constant chemical potential of 2‐chloroethanol. Sodium poly(α‐L‐glutamate) and poly(α‐L‐glutamic acid) are both preferentially hydrated in the whole range of solvent composition. A dehydration process occurs during the 2‐chloroethanol‐induced coil‐to‐helix transition of sodium poly(α‐L‐glutamate). This dehydration process was attributed to the release of some moles of water from the neighborhood of the peptide bond during the nucleation of the helix. After the conformational transition, sodium poly(α‐L‐glutamate) is solvated by one 2‐chloroethanol molecule. The location of water and 2‐chloroethanol molecules in the different parts of the residue (more polar and less polar portions) is also discussed.
Investigation on oligo‐ and polygalacturonic acids by potentiometry and circular dichroism
Authors: Ravanat G. , Rinaudo M. 
Published: December 2004

AbstractThe potentiometric data concerning the dependence of the apparent pK with the degree of neutralization and the nature of counterions (Na or Ca) of galacturonic oligomers and polymers are discussed. They are characterized by an apparent charge density λapp which predicts their electrostatic behavior. The calculated osmotic coefficients from Katchalsky and Manning's theories are in good agreement with the experimental data obtained by potentiometry. The dependence of the osmotic coefficient (ϕCa) as a function of the polymer concentration is established by potentiometry and interpreted in terms of a multichain aggregation. In addition, it is proven that no Ca2+ is ever fixed in excess of stoichiometry. The dependence of CD spectra obtained under the same conditions as the pK measurements shows analogies between the two sets of results. The CD data, in agreement with 13C‐nmr measurements, suggest that in dilute solutions the polymer adopts two conformations: one (acidic form) which may be represented by threefold screw symmetry and a second (Na or Ca form) which can be related to a twofold screw symmetry. The twofold screw symmetry is known to allow the formation of cooperative “egg‐box” fixation of Ca without conformation change.
Diffusion coefficients for rigid macromolecules with irregular shapes that allow rotational‐translational coupling
Authors: Wegener William A. 
Published: December 2004

AbstractWe consider six‐dimensional diffusion and frictional tensors for a rigid macromolecule immersed in a viscous fluid at low Reynolds number. Our treatment allows for screwlike properties which couple rotational and translational movements. We show that the center of diffusion of a screwlike body can be distinct from its hydrodynamic center of reaction. Symmetry conditions which ensure coincidence are examined. The center of diffusion is found to be the point of a body with the slowest diffusive movements, while rotations about the center of reaction encounter the least average resistance. The macroscopic translational diffusion coefficient is evaluated from a perturbation analysis of the six‐dimensional diffusion equation. We show that methodologies which ignore translational–rotational coupling will necessarily underestimate the diffusion rate of screwlike particles. A procedural framework is presented to calculate diffusion coefficients of complicated bodies. As an example we treat a long bent rod.
Enantiomer selection in the addition reaction of optically active 3‐methyl‐5‐substituted hydantoins to N‐[(S)‐α‐methylbenzyl]glycine N‐Carboxyanhydride: Model Reaction for the Stereoselective Polymerization of α‐amino acid N‐carboxyanhydride
Authors: Hashimoto Yutaka , Imanishi Yukio 
Published: December 2004

AbstractIn order to investigate the contribution from the chiral penultimate unit to the enantiomer selection in the activated N‐carboxyanhydride (NCA) polymerizations, the addition reaction to N‐[(S)‐methylbenzyl]glycine NCA of various α‐amino acid hydantoins activated by the tertiary amines was investigated in different solvents. The reactions of activated Ala, Val, and Phe hydantoins were stereoselective and suggested the participation of the penultimate unit in the enantiomer selection of the activated NCA type of polymerization. The degree of enantiomer selection was not well correlated with the structure of hydantoins. Taking into account the dipole repulsion and the orbital overlapping between the reaction species, the transition‐state model was proposed, which gave a good explanation of the selectivity for (R)‐hydantoin in PhNO2 and CH3CN and the selectivity for (S)‐hydantoin in AcNMe2 and HCONMe2. In these two types of solvents the orientation of the methylbenzyl group with respect to the NCA ring is so different that the direction of the approach of the activated hydantoin to the NCA is different. This difference leads to the inversion of enantiomer selection in amide solvents and in others. Cationic species derived from tertiary amines and the chiral amide compound were found to affect the enantiomer selection in the model reaction. The implications of these findings with regard to enantiomer selection in the activated NCA type of polymerization are discussed.
Proton and phosphorus nmr investigation of the conformational states of acid polyadenylic double helix
Authors: Lerner Deborah B. , Kearns David R. 
Published: December 2004

AbstractProton and phosphorus nmr have been used to investigate the double‐helical structures of polyriboadenylic acid [poly(A)] formed in acidic solutions (pH < 6). The results obtained at low pH (∼4.5) are consistent with the model for the acid poly(A) double helix proposed by Rich [Rich, A., Davies, D. R., Crick, F. H. C. & Watson, J. D. (1961) J. Mol. Biol. 3, 71–86]. Other models that have been proposed are inconsistent with the nmr data. The nmr measurements have also been used to examine the conformation of poly(A) helix in the half‐protonated state. Although the base‐stacking arrangement of this state is similar to that observed in the more extensively protonated low‐pH state, the phosphate backbone conformation is different from that found in either the neutral or low‐pH structures.
Vacuum‐ultraviolet circular dichroism of acetylated glucans
Authors: Stipanovic Arthur J. , Stevens E. S. 
Published: December 2004

AbstractWe have measured the solution and film vacuum ultraviolet circular dichroism of a series of acetylated glucans containing α‐ and β‐(1→3), (1→4), and (1→6) linkages. In addition to the 210‐nm band studied previously, we observe the entire π‐π* band near 190 nm; these bands are negative for all triacetates regardless of configuration and conformation. A band near 170 nm shows configurational sensitivity for (1→3)‐ and (1→6)‐linked polysaccharides. The band is positive for both (1→4)‐linked triacetates, but when cellulose triacetate is partially deacetylated, the 170‐nm band becomes negative, thus making the correlation complete. The positive 170‐nm band in cellulose triacetate films is more than an order of magnitude more intense than in any other case and, further, is accompanied by an equally large negative band near 153 nm, raising the possibility that the dichroism in the triacetate arises from strong excitonic interactions which are disrupted upon partial deacetylation.
Structure of cellulose II hydrate
Authors: Lee David M. , Blackwell John 
Published: December 2004

AbstractA hydrate of cellulose II can be formed by swelling Fortisan fibers in hydrazine and then washing in water. The hydrate is stable at 93% relative humidity and has a monoclinic unit cell with dimensions a = 9.02 Å, b = 9.63 Å, c = 10.34 Å, and γ = 116.0°; the space group is P21. The unit cell contains disaccharide sections of two chains and approximately four water molecules. The structure was refined using the LALS method, based on 10 observed and 10 unobserved reflections. An antiparallel arrangement of adjacent chains was assumed, since this occurs in cellulose II (the starting material), and the hydrate also reverts to cellulose II on dehydration. Refinement of the positions and side‐chain conformations of the chains shows that the chains are stacked in the same way as in cellulose II, and the hydrate is formed by insertion of water molecules between the stacks. However, all efforts to arrange the water molecules in crystallographically regular positions led to unsatisfactory agreement between the observed and calculated intensities. These results suggest an irregular arrangement of the water molecules, which was modeled using water‐weighted atomic scattering factors. The analysis resulted in two refined models with relative chain staggers of ∼ +c/4 and ∼ ‐c/4, which are indistinguishable in terms of the x‐ray agreement. Our preference is for the +c/4 model, for which the stacks of chains are analogous to those in cellulose II.
Comparison of Poisson‐Boltzmann and condensation model expression for the colligative properties of cylindrical polyions
Authors: Klein Barbara Kure , Anderson Charles F. , Record M. Thomas 
Published: December 2004

AbstractClosed‐form expression have been derived for the polyelectrolyte contribution to the colligative properties of solutions containing rodlike polyions in the presence of excess added salt. The derivations are based on: the conventional Poisson‐Boltzmann equation for cylindrical symmetry; the thermodynamics of the cell model developed by Marcus [J. Chem. Phys. 23, 1057–1068 (1955)]; and an equation derived from the cylindrical Poisson‐Boltzmann cell model by Anderson and Record [Biophys. Chem. 11, 353–360 (1980)]. Subject to the inherent limitations of the Poisson‐Boltzmann approximation [Fixman (1979) J. Chem. Phys. 70, 4995–5005], the resulting expressions are nevertheless applicable outside the “limit of infinite dilution.” They conform over a range of salt concentrations to the limiting laws deduced by Manning from the hypothesis of counterion condensation [J. Chem. Phys. 51, 924–933 (1969)]. This hypothesis is found to be compatible with the Poisson‐Boltzmann cell model but is not required in the derivation of the thermodynamic coefficients presented here. It is demonstrated that the magnitude of the polyion axial charge density plays a critical role in determining the low‐salt limiting forms of the colligative properties obtained from the Poisson‐Boltzmann equation, in close analogy with Manning's model.
Dielectric studies of aqueous solutions of poly(L‐glutamic acid)
Authors: Nakamura Haruki , Wada Akiyoshi 
Published: December 2004

AbstractThe dielectric features of poly(L‐glutamic acid) are studied by the Fourier synthesized pseudorandom noise method in a time domain combined with a four‐electrode cell. Polymer concentration dependence, the effect of the solvent viscosity, salt effects, and pH dependence are studied concomitantly with measurements of CD. A helix‐to‐coil transition occurs near pH 5.6 for a salt‐free solution; at higher pH values, the polymer has an ionized random‐coil conformation, and at lower pH, it has a deionized α‐helical conformation. When it is in the ionized random‐coil conformation, with the usual features of an electrolytic polymer, the solution shows a relaxation spectrum with a large dielectric increment at low frequencies. In the deionized α‐helical state, no distinct relaxation curves are obtained, which does not deny the existence of a permanent peptide dipole. The pH dependence of the dielectric increment does not mainly correspond to the conformational change from helix to coil, but rather corresponds to the change of chain expansion on account of a charge–charge interaction under low ionic strength, which is conceived of by a viscosity measurement.
Studies of nucleotide conformations and interactions. The relative stabilities of double‐helical B‐DNA sequence isomers
Authors: Kollman Peter A. , Weiner Paul K. , Dearing Andrew 
Published: December 2004

AbstractWe present the results of molecular‐mechanics studies on base‐paired dinucleoside phosphates and hexanucleoside pentaphosphates. Starting from B‐DNA‐like conformations, we have refined the nucleic acid conformations, allowing all degrees of freedom to relax. The calculated energies of different base sequences are used to investigate the basis for the different stabilities of DNA polymers of different sequences, as found by Wells et al. [J. Mol. Biol. 54, 465–497, 1970]. Our calculations appear to reproduce the relative melting temperatures of sequence isomers as well or better than any of the previous calculations which addresssed the question of nucleotide stability. We offer a detailed physical explanation of three observations, that poly(dA)·poly(dT) melts higher than poly[d(A‐T)]·poly[d(A‐T)] by 6°C, that poly(dG)·poly(dC) melts lower than poly[d(G‐C)]·poly[d(G‐C)] by 12°C, and that poly(dA‐dG)·poly(dT‐dC) melts lower than poly(dA‐dC)·poly(dT‐dG) by 6°C. The dihedral angles found after refinement are similar to those of Levitt [Proc. Natl. Acad. Sci. USA 75, 640–644, 1978] and differ by ∼20° from the B‐DNA values. We also see evidence of base tilting and twisting similar to that found by Levitt. The two main differences in the results of our calculations and Levitt's lie in the sugar puckers [we find mainly C(2′)endo] and in the tendency to stay in local “torsional” minima (we find a number of examples of C(3′)endo sugar puckering and ω′ = trans rather than gauche). Both of these results are dependent on the nature of the potential function used in our study. However, our finding of movement from local torsional minima is suggestive of the significant flexibility of double‐stranded deoxynucleotides.
Methacrylate polymerization by azoRNA: Potential usefulness for chromosomal localization of genes
Authors: Hartman Rosemarie F. , Brown Gary L. , Rose Seth D. 
Published: December 2004

AbstractAn azo pyrimidine nucleotide has been prepared and enzymatically attached to oligo(A) primers. The nucleotide's azo pyrimidine group has previously been shown to initiate polymerization of methacrylate esters designed to bind marker groups for visualization by microscopy. When attached to RNA molecules complementary to a chromosomal DNA segment, these nucleotides may allow localization of the DNA segment following in situ hybridization of the probe, methacrylate polymerization, and marker attachment. Since mRNA molecules of potential interest as probes bear a 3′‐poly(A) tail, the modified nucleotides were added to oligo(A) primers as models. First, N4‐ureidocytosine nucleotides were enzymatically added to ApApA, (Ap)9A, or [5′‐32P]‐(pA)10, using the modified cytidine 5′‐diphosphate and “primer‐dependent” polynucleotide phosphorylase (M. luteus). In the case of the ApApA‐primed reaction, the N4‐ureidocytosine nucleotides in the product polynucleotide were converted into azo nucleotides by oxidation with N‐bromosuccinimide. The other two primers were employed to study the time course of polynucleotide formation and to verify that primer was indeed being utilized by the enzyme. The suitability of the modified nucleotide for in situ hybridization studies was examined. Poly(N4‐ureidocytidylic acid) was prepared from poly(C) and semicarbazide by the bisulfite‐catalyzed transamination reaction. It was found that 95% of the N4‐ureidocytosine nucleotides in this polynucleotide survive the elevated temperatures typically required for DNA:DNA denaturation and RNA:DNA annealing. When poly(N4‐ureidocytidylic acid) was mixed with poly(I) in buffered aqueous salt solutions, no evidence for hybridization was found, so binding of the probe RNA to the denatured chromosomal DNA molecule via the modified nucleotides is not expected. Upon oxidation of poly(N4‐ureidocytidylic acid) with N‐bromosuccinimide, the azo nucleotides were formed, as judged by the appearance of a characteristic peak at approximately 350 nm in the uv‐absorption spectrum of the yellow‐orange product, azoRNA. The azo nucleotides in azoRNA exhibited the expected acid lability, which is known to be accompanied by 1‐glyceryl methacrylate polymerization in the case of the simple azo pyrimidine. Because 1‐glyceryl metharcylate bears substituent glycol groups for attaching heavy atoms or fluorescent markers, it is possible that probe RNA molecules bearing azo nucleotides may be useful for localizing low‐multiplicity genes along eukaryotic chromosomes.
Simplified theory of the helix–coil transition in DNA based on a grand partition function
Authors: Lifson Shneior , Zimm Bruno H. 
Published: December 2004

AbstractThe statistical mechanics of the helix–coil transition in DNA is treated by means of a grand partition function. This method is simpler than methods used previously, although it is suitable only in the limit of great chain lengths. Expressions for the number of base pairs bonded are obtained and shown to be identical to those obtained by other methods in the limit of great chain lengths. The physical meaning of the grand partition function is also discussed.
The presence in collagen of γ‐glutamyl peptide linkages
Authors: Franzblau Carl , Gallop Paul M. , Seifter Sam 
Published: December 2004

AbstractA method is described for formation of hydroxamic acids by direct coupling, in aqueous medium, of hydroxylamine hydrochloride and the sodium salt of a carboxylic acid. The reaction is mediated by a water‐soluble carbodiimide, 1‐cyclohexyl‐3‐[2‐morpholinyl‐(4)‐ethyl]‐carbodiimide metho‐p‐toluene sulfonate. Using model compounds, the production of α‐, β‐ and γ‐acyl hydroxamic acids was studied. Hydroxamic acid derivatives of α‐polyglutamic and γ‐polyglutamic acids were also prepared. Dinitro‐phenylhydroxamate derivatives were prepared and subjected to Lossen rearrangement, and the reaction mixtures hydrolyzed. Analysis showed that α‐polyglutamic acid yielded as many molecules of α,γ‐diaminobutyric acid as there had been glutamic acid residues in the form of the dinitrophenylhydroxamate, and gave rise to no ammonia and succinic semialdehyde. In contrast, γ‐polyglutamic acid yielded exactly twice the molar quantity of ammonia as there had been glutamic acid residues in the form of dinitrophenylhydroxamate, and also gave rise to significant quantity of succinic semi‐aldehyde but no α,γ‐diaminobutyric acid. Since production of the latter is characteristic of α‐glutamyl hydroxamates and production of the former is associated with γ‐glutamyl hydroxamates, the results indicated that the side‐chain carboxyl groups of either polymer retained their identities during formation of the hydroxamic acid derivative, and no interchange had occurred between α‐ and γ‐carboxyl groups. These methods were then used to establish that gelatin of ichthyocol contains (per 1000 total residues) at least 20 residues of glutamic acid in γ‐peptide linkage. Due to the incomplete dinitrophenylation of the hydroxamic acid derivative of the protein, gelatin of calf skin collagen gave a lower figure of 10 such linkages per 1000 total amino acid residues–a value which must be considered a minimum value. These results show that γ‐glutamyl peptide bonds exist in collagen.