bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ionic polysaccharides. V. Conformational studies of hyaluronic acid, cellulose, and laminaran
Authors: Cleland Robert L. 
Published: December 2004

AbstractHindered rotation was studied for the disaccharides composed of basic β‐glucopyranose units A (linked at O1 and O4) and B (linked at O1 and O2) in Cl conformation. The van der Waals' interactions were calculated for the Lennard‐.Jones, Buckingham, and Kitay‐gorodsky interatomic potential functions, including a study of the effect of minimization of the first two functions for each atomic pair k, m (a) at the sum rkm* of the usual crystal atomic radii rk* + rm* and (b) at rkm* + 0.2 Å. Values of the ratio of unperturbed to free‐rotation root‐mean‐square end‐to‐end distance σ, were calculated for chains composed of the unsolvated disaccharide repeating units: AA (cellulose), AB and BA (hyaluronic acid), and BB (laminaran). For cellulose and hyaluronic acid, σ increases markedly with both assumed atomic radii rk* and θ, the supplement of theglycosidebond angle. Energy contributions from dipole–dipole and side‐chain interactions cause relatively small dimensional changes for hyaluronic acid: for cellulosic polymers bulky side groups attached near the glycoside carbon atom may increase or decrease unperturbed dimensions, depending on the potential function chosen. Inclusion of bond torsional potentials increases σ for cellulose and hyaluronic acid and decreases σ for laminaran. Hydrogen‐bonding ellects normally increase calculated σ values for unsolvaled polymers. The predicted influence of temperature on σ is small. The large decrease in σ with increasing temperature which appear to occur experimentally for cellulosic polymers are prc.‐umably due to conformational effects of solvation.
Theory of friction‐limited DNA unwinding
Authors: Crothers D. M. , Spatz H. C. 
Published: December 2004

AbstractThe theory of friction‐limited DNA unwinding is developed explicitly for moderate tind large perturbations. This extension of the earlier theory of the relaxation kinetics is necessary because of the complex nature of the rate limitation for small perturbations. The assumption of the theory that is violated under relaxation conditions is that base pairing reactions occurring at a constant local degree of twist of the strands are fast compared to the net unwinding of the molecule. However, these reactions that are slow for small perturbations have a large activation energy, and become faster than friction‐limited un winding for large enough temperature jumps and sufficiently large DXA molecules. Thus only the rate for moderate and large perturbations is clearly limited by frictional resistance to turning the molecule in solution. The model used is a diffusional unwinding of the two strands, driven by the accompanying decrease in free energy. For large perturbations a numerical solution of the diffusion equation is required, since the diffusion coefficient is not constant. Two new parameters must be introduced into the equilibrium statistical theory to describe friction‐limited unwinding kinetics. These are the force constant b, for winding up coil regions and the frictional coefficient per base pair βcfor rotating coil regions in solution. We find by fitting the theory to experiment that b = 1.8 × 10−13 ergs/ rad2‐ and βc = 3.5 × 10−21 erg see/base pair, both for DNA melted in alkali at 0.4.M Na + and ∼30 °C. The latter value is in agreement with predictions based on the viscosity of single stranded DNA in alkali. The quoted value of bcan be interpreted to mean that the number of conformational states of a nucleolide is reduced by an average factor of 1.55 when it is wound around another strand to the degree of twist in a double helix, but without forming a base pair.
Sedimentation characteristics of DNA multiply crosslinked by a difunctional alkylating agent, mustard gas
Authors: Edwards P. A. , Shooter K. V. 
Published: December 2004

AbstractIt is confirmed from sedimentation studies that only a small fraction of diguaninyl derivatives formed on reaction on reactions of native DNA with mustard gas crosslink the two DNA chains. It is also apparent that heavily alkylated DNA can be studied in the denatured form in dimethyl sulfoxide without the gross degradation that results if denaturation is effected by alkali.
Specificity in the genetic code: the role of nucleotide base–amino acid interaction
Authors: Rendell Marc S. , Harlos J. P. , Rein Robert 
Published: December 2004

AbstractThe mechanism of the unique and specific association of a given amino acid to its t‐RNA is investigated by theoretical methods. Several possible schemes are proposed to explain specificity. The physical forces which act within these mechanisms are illustrated by the computer simulation of probable interactions between glycine and nucleotide bases and base pairs. It is demonstrated that glycine has direct and selective affinities for the nucleotide bases and that these interactions are principally determined by the polar groups. Energies have been calculated for the interaction of glycine with several base pairs. From these, the possibility that specificity arises through direct complexing of an amino acid with its anticodon is evaluated.
Thermodynamic parameters of helix‐coil transition in polypeptide chains I. Poly‐(L‐glutamic acid)
Authors: Bychkoya V. E. , Ptitsyn O. B. , Barskaya T. V. 
Published: December 2004

AbstractThe helix‐coil transitions for poly(L‐glutamic acid) (PGA) in 0.2M NaCl and in its mixture with dioxane were studied by the methods of spectropolarimetry, viscometry, and potentiometric titration at different temperatures from 8 to 50°C. The enthalpy and entropy differences between the helical and coillike states of uncharged PGA molecules were determined from the curves of potentiometric titration. The temperature dependence of the cooperativity parameter σ was determined by two methods: from the sharpness of transition and from the dependence of the intrinsic viscosity on the helical content in the transition region. In 0.2MNaCl, σ= (2.5 ± 0.5) × 10−3 and practically does not depend on temperature, i.e., the cooperativity of the helix‐coil transition is connected mainly with the entropy decrease in initiating helical regions (ΔSi ≈ −12 is mole of helical regions). On the contrary, initiation of a helical region in the water‐organic solvent mixture is accompanied by a considerable enthalpy increase.
Biosynthèse de la cellulose bacterienne deutériée: étude par R. M. N. du taux d'incorporation et de la localisation du deutérium
Authors: Barnoud Fernand , Gagnaire Didier , Odier Léon , Vincendon Marc 
Published: December 2004

AbstractThe use of the NMR spectra (250 MHz) of cellulose triacetate allows the determination of the percentage of deuterium bonded to each of the six carbon atoms of the monomer residue (except for H−1 and one of the protons bonded to C6 where the signals overlap). Deuterated derivatives of D‐glucose and/or deuterated water were used for the biosynthesis of bacterial cellulose by Acetobacter xylinum. Analysis of NMR spectra of acetylated samples gives the following results. About 90% of the protons linked to C1 and C6 come from the D‐glucose used in the nutrition medium, whereas 10% are exchanged with other sources of protons. Over 40% of the protons linked to C2, C3, C4, and C5 arise from the water of the nutrition medium. Discrepancies between results of biosynthesis from deuterated water and from deuterated D‐glucose can only be explained if more than one enzymatic process is involved in the biosynthesis of bacterial cellulose.
Eleclrooptical study of the electric polarizability of rodlike fragments of DNA
Authors: Hornick C. , Weill G. 
Published: December 2004

AbstractThe anisotropy of electrical polarizability of rodlike fragments of DNA has been studied by a number of electro‐optical methods: Kerr effect (combined with flow birefringence), light scattering, diehroism, and fluorescence in an electric field. The most sensitive technique (Kerr effect) has been used to study the variation of the polarizability with the nature and concentration of counteroins. DNA fragments constitute a truly rigid polyelectrolyte of known structure. The value obtained can then be quantitatively compared to the predictions of those of the theories of the longitudinal polarizability of rigid polyelectrolytes which are based on true molecular parameters. The comparison emphasizes the role of the counterion–counterion repulsion. Oosawa's theory seems to represent the best approach but fails to explain the differences observed between monovalent and divalent ions.
Far‐infrared spectra of some globular proteins
Authors: Buontempo U. , Careri G. , Fasella P. , Ferraro A. 
Published: December 2004

AbstractThe far‐infrared absorption spectrum (40–400 cm−1) of solid pellets and films of several globular proteins (lysozyme, myoglobin, hemoglobin, serum albumin, ribonuclease, chymotrypsinogen, subtilisin) and of some representative polypeptides [nylon 66, poly (γ‐benzyl L‐glutamate)] have been investigated by using a Michelson interferometer. While polypeptides are known to present several peaks which can be assigned mostly to hydrogen‐bond modes, all the investigated globular proteins display only one broad, intense baud in the 100–200 cm−1 region. The origin of this band, which persists even after denaturation or partial digestion, is discussed.
Light‐scattering and potentiometric‐titration studies of poly‐L‐tyrosine in aqueous solution
Authors: Senior Marilyn B. , Gorrell Sandra L. H. , Hamori Eugene 
Published: December 2004

AbstractAqueous solutions of poly‐L‐tyrosine were studied by potentiometric titrations, light‐scattering measurements, and infrared spectroscopy in order to characterize the conformational changes the macromolecules exhibit when the hydrogen‐ion concentration of the solutions is varied. It was found that when the pH of the system at 25°C is lowered from a value of about 13 the poly‐L‐tyrosine molecules undergo a random‐coil to β‐structure conformation change at pH 11.5. It appears, that under the experimental conditions used, the formation of the β structure is an intramolecular process which involves the folding of the polymer backbone into several hairpins of antiparallel β structure. On further lowering of the pH of the solutions aggregation (pH 11.35) and subsequently precipitation (pH 11.2) takes place. Since the apparent pK of the polymer does not show a drastic change during the random‐coil to β‐structure conformation change, it was concluded, that the therinodynamic driving force for this conformation change is mainly due to the electrostatic effect of the partially charged side chains of the poly‐L‐tyrosine molecules.
The binding of Mg++ ions to polyadenylate, polyuridylate, and their complexes
Authors: Krakauer Henry 
Published: December 2004

AbstractThe binding of Mg ++ to polyadenylate (poly A), Polyuridylate(poly U), and their complexes, poly (A + U) and poly (A + 2U), was studied by means of a technique in which the dye eriochrome black T is used to measure the concentration of free Mg−. The apparent binding constant KX = [MgN]/[Mg++][N], N = site for Mg++ binding (the phosphate group of the nucleotide), was found to decrease rapidly as the extent of binding increased and, at low extents of binding, as the concentration of Na− increased in poly A, poly (A + U), and poly (A + 2U), and somewhat less so in poly U. Kx is generally in the range 104 > KX > 102. The cause of these dependences is apparently, primarily, the displacement of Na+ by Mg++ in poly U and poly (A + U) on the basis of the similarity of extents of displacement measured in this work and those measured potentiometrically.

was calculated and was found to approach zero as the concentration of Na+ increased. In poly U, poly (A + U), and poly (A + 2U) at low ΔH′ v.H. > 0, about + 2 kcal/“mole.” In poly A, also at low salt, ΔH′ v.H. ≈ −4 kcal/“mol” for the initial binding of Mg++, and increases to +2 kcal/“mol” at saturation. This enthalpic variation probably accounts for the anticooperativity in the binding of Mg++ not ascribable to the displacement of Na++.
Volume changes accompanying the complex formation of polyadenylic and polyuridylic acids
Authors: Noguchi Hajime , Arya Suresh K. , Yang Jen Tsi 
Published: December 2004

AbstractThe complex formation of polyadenylic acid (poly A) and polyuridylic acid (poly U) in 0.1M NaCl solution containing 0.01M sodium cacodylate was followed by dilatometric measurements at various mixing ratios of poly A and poly U. The volume changes, ΔV, accompanying the formation of poly A. poly U and poly A.2poly U were + l.5 and + 2.5 ml per mole of the nucleotide residue, respectively. This increase in volume was probably due to the increased counterion binding when the single‐stranded polynucleotides were converted into the double‐ and triple‐stranded helices, since depletion of charged species from the solvent proper would lessen the effect of electrostriction, thus resulting in a positive ΔV. The conversion of a single‐stranded poly A to a double‐stranded helix in acidic solution led to a ΔV of + 3.8 ml per mole of the nucleotide residue. This increase in volume was attributed to the charge neutralization as a result of protonation of the adenine bases.
Potentiometric titration of poly‐S‐carboxyethyl‐L‐cysteine
Authors: Maeda Hiroshi , Ikeda Shoichi 
Published: December 2004

AbstractPotentiometric titration curves have been determined for aqueous solutions of poly‐S‐carboxyethyl‐L‐cysteine, which is subject to the β‐coil transition by a change in pH. Reversibility and time dependence of the titration curves are examined by different methods in order to establish the conditions for obtaining equilibrium curves. The β‐coil transition is manifest, at some region on the equilibrium titration curve, if pH – log (α/1 – α) is plotted against α. Assuming a value, 4.00, for pKint, the free‐energy change for the β‐coil transition of uncharged polymer has been evaluated from the extrapolation of the observed titration curves and is found to depend on the ionic strength and polymer concentration. The Henderson‐Hasselbach plot of the titration curve yields clearer distinction between the β‐form and random coil, and it permits estimation of the content of β‐form at, a given pH. Comparison of the conformational titration curve with the circular dichroic measurements leads to a value of −10,000° for [θ]223 for the pure β‐structure. Precipitation which occurs at low degrees of ionization and, especially, at high ionic strength does not reveal any discontinuous change of the titration curve, which suggests that, the degree of ionization of the precipitated β‐form is not very different from that in solution.
Nuclear magnetic resonance and optical spectroscopic studies of block copolymers of polypeptides. I. Block copoly[(benzyl‐L‐glulamate)n: (benzyl‐L‐aspartate)m]
Authors: Paolillo L. , Temussi P. , Trivellone E. , Bradbury E. M. , Crane‐Robinson C. 
Published: December 2004

AbstractIn a study of A–B type block copolymers of γ benzyl‐L‐gultamate and β‐benzyl‐L‐aspartate use has been made of the observations: (1) that for poly aspartate esters the chemical shifts of the α‐CH and NH resonances are sensitive to the helix sense, (2) that in both helical and random coil conformations the same resonances of poly‐γ‐benzyl‐L‐glutamate are well separated from those of poly aspartates. Since the sense of poly‐β‐benzyl‐L‐aspartate is very sensitive to the inclusion of γ‐benzyl‐L‐glutamate residues, the degree of overlap between the blocks can be studied by monitoring the helix sense of the aspartate. The ability of the NMR method to make separate observation of the two blocks removes the necessity of relying on an overall ORD parameter such as b0. The copolymers studied include those having lefthanded, righthanded, and mixed‐sense aspartate, corresponding to differing degrees of overlap.
Ca2+‐induced conformational transitions of phosphorylated peptides
Authors: Hollöasi M. , Ötvös L. , Ürge L. , Kajt´ar J. , Perczel A. , Laczkó I. , Vadász ZS. , Fasman G. D. 
Published: December 2004

AbstractCD spectroscopic studies on protected peptides containing lysine and serine, or phosphoserine, and on serine‐containing fragments of the neurofilament protein midsized subunit, both in the unphosphorylated and phosphorylated form, are reported. The introduction of the phosphoryl group was not found to have a significant spectral effect in aqueous solution. In trifluoroethanol (TFE), spectral shifts toward unordered (type U) spectra or the appearance of distorted spectra likely reflect the adoption of aperiodic polypeptide conformations due tosalt bridge(s)between negatively charged phosphoserine and positive lysine side‐chain groups. A turn‐stabilizing effect of phosphorylation was also observed.CD‐monitored titration experiments in TFE revealed a high conformational sensitivity of phosphopeptides toward Ca2+ions. The appearance of the unordered spectra or spectral shifts were the sign of a bulkdisorderingeffect of Ca2+ions. Spectra with specific spectroscopic features reflect the formation of Ca2+complexes and the adoption of ordered unique backbone conformations.When ordered structures were obtained on addition of Ca2+ions, the observed CD curves showed a resemblance to the spectrum of β‐pleated sheets. This may originate fromchain extensionand the formation of β‐pleated sheet segments fixed by Ca2+bridges between PO3Hgroups of adjacent peptide chains. The data clearly show that the effect of the Ca2+ions is highly specific: the sequence, chain length, presence and distribution of charged side‐chain groups, degree and site of phosphorylation, and environmental factors appear to be determining in the process of chain extension or β‐sheet formation. © 1993 John Wiley & Sons, Inc.
Transient electric birefringence of agarose gels. I. Unidirectional electric fields
Authors: Stellwagen John , Stellwagen Nancy C. 
Published: December 2004

AbstractThe orientation of agarose gels in pulsed electric fields has been studied by the technique of transient electric birefringence. The unidirectional electric fields ranged from 2 to 20 V/cm in amplitude and 1 to 100 s in duration, values within the range typically used for pulsed field gel electrophoresis (PFGE). Agarose gels varying in concentration from 0.3 to 2.0% agarose were studied. The sign of the birefringence varied randomly from one gel to another, as described previously [J. Stellwagen & N. C. Stellwagen (1989), Nucleic Acids Research, Vol. 17, 1537–1548]. The sign and amplitude of the birefringence also varied randomly at different locations within each gel, indicating that agarose gels contain multiple subdomains that orient independently in the electric field. Three or four relaxation times of alternating sign were observed during the decay of the birefringence. The various relaxation times, which range from 1 to ∼ 120 s, can be attributed to hierarchies of aggregates that orient in different directions in the applied electric field. The orienting domains range up to ∼ 22 μm in size, depending on the pulsing conditions.The absolute amplitude of the birefringence of the agarose gels increased approximately as the square of the electric field strength. The measured Ker constants are ∼ 5 orders of magnitude larger than those observed when short, high‐voltage pulses are applied to agarose gels. The increase in the Kerr constants in the low‐voltage regime parallels the increase in the relaxation times in low‐voltage electric fields. Birefringence saturation saturation curves in both the low‐ and high‐voltage regimes can be fitted by theoretical curves for permanent dipole orientation. The apparent permanent dipole moment increase approximately as the 1.6 power of fiber length, consistent with the presence of overlapping agarose helices in the large fiber bundles orienting in low‐voltage electric fields, the optical factor is approximately independent of fiber length. Therefore, the marked increase in the Kerr constants observed in the low‐voltage regime is due to the large increase in the electrical orientation factor, which is due in turn to the increased length of the fiber bundles and domains orienting in low‐voltage electric fields. Since the size of the fiber bundles and domains approximates the size of the DNA molecules being separated by PFGE, the orientation of the agarose matrix in the applied electric field may facilitate the migration of large DNA molecules during PFGE. © 1994 John Wiley & Sons, Inc.
Conformational analysis of chitobiose and chitosan
Authors: Yui Toshifumi , Kobayashi Hisayoshi , Kitamura Shinichi , Imada Kiyohisa 
Published: December 2004

AbstractThe relaxed potential energy surfaces of chitobiose were calculated based on the MM3‐force field by optimizing dimer structures on a 10° grid spacing of the torsional angles about the glycosidic bonds (Φ,Ψ). The 36 conformations; the four combinations of the hydroxymethyl group orientations coupled with the nine of the secondary group ones— were assumed for each Φ,Ψ conformation. The four conformations, each differing in the hydroxymethyl group orientations, were considered for the whole Φ,Ψ space, and all the 36 conformations, for the restricted space of low energy. While the resulting energy map and the structures of the energy minima were similar to those proposed for cellobiose in many respects, more restricted energy profile was suggested for the relaxed map of chitobiose where differences in the energy level between the global minimum and the local minima were within 5.4 kcal/mol, compared with the equivalent value of 3.6 kcal/mol for cellobiose. Further depression of the global minimum occurred when the acidic residue was used. The Monte Carlo samples of the chitosan chain were generated based on the relaxed map to predict the unperturbed coil dimension in solution. The chitosan chains showed Gaussian behavior at x = 500 (x, degree of polymerization) and gave the characteristic ratio Cx, of about 70, which was much larger than the experimental values observed for the chitosan and cellulosic chains. © 1994 John Wiley & Sons, Inc.