bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chain association of pectic molecules during calcium‐induced gelation
Authors: Thibault J. F. , Rinaudo M. 
Published: December 2004

AbstractThe chain association of pectic molecules with different levels and patterns of esterification during calcium‐induced gelation was studied by methods such as light scattering, viscometry, and determination of calcium activity coefficient and of calcium transport parameter. A gel point can be determined, assuming a power law including a critical ratio (equivalent concentration of calcium ions/pectin carboxylic groups) and quasi‐critical exponents varying in the range 0.50–1.26. The values of these critical parameters were discussed as a function of polymer concentration, of level and pattern of esterification, and of the nature of the divalent counterion. The lower these values are, the better, apparently, the gel‐forming ability of the pectins is.
DNA orientation during gel electrophoresis and its relation to electrophoretic mobility
Authors: Hurley Ian 
Published: December 2004

AbstractIntensities of polarized fluorescence from ethidium bound to phage λ DNA undergoing agarose gel electrophoresis were measured. The intensities were strongly field dependent at voltage gradients of 8 V/cm, consistent with a partial orientation of DNA helices in the direction of electrophoresis about 500 times larger than seen in the same field in solution. Such an orientation was predicted by a reptation model of gel electrophoresis advanced by Lumpkin et al. [(1985) Biopolymers, 24, 1573–1593]. The present results can be fit successfully to this theory with a single adjustable parameter, the gel–DNA contact distance. Also, λ DNA electrophoretic mobilities in the same concentration gel were determined using the same buffer system. Both orientation and mobility measurements can be fit to the reptation theory within a factor of two using the same values of two parameters, the gel–DNA contact distance and the ratio of DNA charge to frictional coefficient.
Halogenated nucleic acids: Effects of 5‐fluorouracil on the conformation and properties of a polyribonucleotide and its constituents
Authors: Loomis Ronald E. , Alderfer James L. 
Published: December 2004

AbstractThe conformational properties of 5‐fluorouracil derivatives are compared to uracil derivatives. FUrd, 5′‐FUMP, and poly(FU) are studied as a function of pH and temperature by 19F‐ and 1H‐nmr spectroscopy, and the corresponding uracil derivatives by 1H‐nmr spectroscopy. FUrd exhibits no significant conformational changes with solution pH (5–10). In contrast, at low pH (6–7) 5′‐FUMP and 5′‐UMP show similar conformational features, while at high pH (9) 5′‐FUMP shows significant conformational alterations. Also, poly(U) and poly(FU) are conformationally similar at low pH, but increasing pH induces changes in poly(FU). These changes are observed in the backbone [γ(C4′‐C5′)], furanose, and furanose‐base conformations. The apparent pKa of N3‐H ionization of the FUra base is determined by 1H‐ and 19F‐nmr to range from 7.5 to 8.2 [FUrd < 5′‐FUMP < 5′‐FUDP < poly(FU)]. These observations are interpreted as a result of electrostatic interactions generated between the ionized phosphate group and the negatively charged base moiety as the pH is raised. The interaction properties of poly(FU) with ApA are studied by 1H‐ and 19F‐nmr spectroscopy, and these properties compared to those published for poly(U). Poly(FU) forms a complex with ApA inducing upfield 1H‐shifts in both components, and downfield 19F‐ shifts in poly(FU). The base stoichiometry of the complex for poly(U)·ApA is 2U:1A at various U/A ratios. In contrast, the base stoichiometry of the poly(FU)·ApA complex appears to be dependent on the FU/A ratio. At high FU/A ratio, the complex is 2FU:1A, and as the FU/A ratio approaches unity the complex becomes 1FU:1A.
Sequential polypeptides containing arginine as histone models: Synthesis and conformational studies
Authors: Panoy‐Pomonis Eugenia , Sakarellos Constantinos , Sakarellos‐Daitsiotis Maria 
Published: December 2004

AbstractThe sequential polypeptides (L‐Arg‐X‐Gly)n, where X represents amino acid residues Ala, Val, and Leu, were prepared as models of arginine‐rich histones to be used in studying their structure and their interactions with DNA. The polymerization was carried out on the pentachlorophenyl active esters of the appropriate tripeptides, while the toluene‐4‐sulfonyl group was used for protecting the arginine guanido group. CD was employed to investigate the conformation of (L‐Arg‐X‐Gly)n polymers in aqueous solutions, at different pH, as well as in trifluoroenthanol and hexafluoroisopropyl alcohol solutions. In aqueous solutions (at pH 7 and 12) the prepared sequential polymers behaved as a random coil. The CD spectra in various trifluoroethanol–water or hexafluoroisopropyl alcohol–water mixtures indicated that the degree of helical conformation of the studied polytripeptides increased in the order of Ala → Val → Leu. The opposite was true for the β‐structure. Characteristics of β‐turn are excluded from the poly(L‐Arg‐L‐Leu‐Gly), which assumed the most pronounced helical conformation. The poly(L‐Arg‐L‐Val‐Gly) exerts a significant preference to the β‐turn structure compared to that of poly(L‐Arg‐L‐Ala‐Gly). Thus the probability for helical, β‐structure or β‐turn conformations of the polymers was analyzed in relation to the bulkiness and length, and to the special features of the X‐residue side chain (β‐branching). We concluded that the prepared sequential arginine‐containing polypeptides are plausible models for histone fractions, f3 and f2α1.
Picosecond relaxations in model substances for proteins: A millimeter‐wave investigation on crystalline alkyl amides
Authors: Häseler S. , Poglitsch A. , Genzel L. , Kremer F. 
Published: December 2004

AbstractThe dielectric absorption at millimeter‐wave (mm‐wave) frequencies (50–150 GHz) of N‐methylacetamide (NMA), N,N‐dimethylacetamide (DiNMA), and N,N‐dimethylacrylamide (DiNMAcry) is measured. Measurements are performed using the oversized‐cavity technique in the temperature range from liquid helium to room temperature. Additionally, a mm‐wave interferometeric measurement at room temperature is made. NMA and DiNMAcry exhibit monotonic increases of the absorption coefficient with temperature as well as with frequency. For DiNMA a monotonic increase of the absorption coefficient with frequency is also found, while the absorption coefficient as a function of temperature shows a pronounced maximum at approximately 30 K. At this maximum the absorption coefficient of DiNMA exceeds those of NMA and DiNMAcry by about two orders of magnitude. The dielectric behavior of the three substances can be described by relaxation processes in asymmetric double‐well potentials. For the low‐temperature relaxation in DiNMA the double well could be established by two possible positions of the molecule in the crystal that are separated by a rotational movement. Hydrogen bonds and long side chains may hinder these relaxational movements in NMA and DiNMAcry, respectively, and thereby account for their comparatively lower absorption. The results are compared with similar results recently obtained on proteins and synthetic biopolymers.
Conformation of dioxopiperazines, II. CNDO/2 quantum mechanical calculations on conformational preferences in cyclo (glycyl‐L‐alanyl), cyclo(glycyl‐L‐valyl), and both epimers of cyclo‐di‐(alanyl)
Authors: Bielinski Henryk , Ciarkowski Jerzy 
Published: December 2004

AbstractConformational energy calculations, aimed at verification of the suitability of the semiempirical molecular orbital CNDO/2 method for conformational elucidations in cyclic dipeptides formed from amino acids with aliphatic side chains, have been carried out. The results obtained for four dioxopiperazines [DOP; cyclo(Glycyl‐L‐Alanyl), cyclo(Glycyl‐L‐Valyl), and both epimers of cyclo‐di‐(Alanyl)] point out very good agreement with experimental premises. The latter include (1) the preference of the cis‐peptide bonds for being nonplanar, which results in twisted‐boat conformations of the DOP ring; (2) greater stability of conformers with a side chain oriented axially over those with a side chain oriented equatorially; (3) the preference of cyclo(Gly‐Val) for assuming a folded conformation with one of the side chain γ‐methyl groups sticking over the DOP ring.
Experimental tests of a geometrical abstraction of fibrin polymerization
Authors: Dietler G. , Känzig W. , Häberli A. , Straub P. W. 
Published: December 2004

AbstractBy combining measurements of the enzymatic release of fibrinopeptide A (FPA) with measurements of intensity and linewidth of Rayleigh scattering from fibrin polymer solutions prior to gelation, we have systematically tested a variety of predictions that can be made on the basis of a simple geometrical abstraction of fibrin polymerization. The experimental investigations include FPA content of fibrin polymers, aggregation of fibrin with fibrinogen, enzyme kinetics, shift of the chemical equilibrium by adding Gly‐Pro‐Arg‐Pro or fibrinogen to the polymer solution, evolution of the polymerization, and influence of fibrinopeptide B release. Among the considered geometrical abstractions there is only one that survives the experimental tests and at the same time is compatible with the electron micrographs by other authors. The main conclusions that can be drawn are (1) the location of binding sites A must be taken from the structure of the fibrinogen molecule proposed by Hoeprich and Doolittle [Biochemistry (1983) 22, 2049–2055], (2) The fibrinogen monomer is basically centrosymmetric, (3) the state of polymerization is reversible and corresponds to a chemical equilibrium, and (4) Michaelis–Menten enzyme kinetics can be applied.
Structure of native proteoglycan aggregates from chick limb‐bud chondrocytes
Authors: Ohno Hiroyuki , Blackwell John , Jamieson Alexander M. , Pechak David G. , Carrino David A. , Caplan Arnold I. 
Published: December 2004

AbstractLaser light‐scattering has been used to investigate the size of native proteoglycan aggregates (PGA‐aA1) from day‐8 chick limb‐bud chondrocyte cultures isolated under associative extraction and purification conditions in 0.4M guanidinium chloride (GdnHCl) solution. Dynamic light‐scattering measurements yielded a hydrodynamic radius, Rs, of 244 ± 10 nm for PGA‐aA1 in 0.4M GdnHCl, and a weight‐average molecular weight (Mw) of 150 ± 50 × 106 was obtained from a Zimm plot. Disaggregation in 4.0M GdnHCl aqueous solution yielded proteoglycan subunits (PGS) with Rs = 39 ± 2 nm, Mw = 1.6 ± 0.3 × 106, which reassembled in 0.4M GdnHCl to form “reconstituted native” aggregates (PGA‐raA1) with Rs = 121 ± 6 nm, Mw = 17 ± 3 × 106. A second specimen of PGA‐aA1 had Rs = 192 ± 10 nm, Mw = 100 ± 10 × 106. The latter value was estimated from an empirical relationship between Mw and Rs. After dissociation, this specimen reassembled to form PGA‐raA1 with Rs = 85 ± 5 nm, Mw = 12 ± 1 × 106. These data are compared with those for a specimen of reconstituted aggregate (PGA‐A1) that had been extracted under dissociative conditions and then reaggregated by dialysis to 0.4M GdnHCl aqueous solution, for which Rs = 138 ± 9 nm, Mw = 45 ± 8 × 106. From these values, we have calculated the weight‐average number of subunits per aggregate Nw: 111 for PGA‐aA1 and 12 for raA1 (70 and 7 for the second PGA‐aA1 and PGA‐raA1 specimen, respectively) as compared to 32 for PGA‐A1. The numbers of subunits per aggregate were also determined from electron micrographs of spread specimens. The latter results show the same trends as those obtained by light scattering, but lead in each case to lower numbers of subunits per aggregate. These data demonstrate conclusively that PGA samples exhibit a higher degree of aggregation in solution than visualized in typical electron microscopy (EM) preparations, probably due to disaggregation during EM specimen preparation. Since Nw determined both by light scattering (LS) and by EM are larger for native versus reconstituted aggregate samples, our data point to a more compact aggregation of subunits along the hyaluronic acid (HA) chains in the former.
Kinetics of nonspecific binding reactions of proteins with DNA flexible coils: Site‐based and molecule‐based association reactions
Authors: Mazur Sharlyn J. , Record M. Thomas 
Published: December 2004

AbstractDomain effects on the pseudo‐first‐order kinetics of the reversible and irreversible association of proteins or other ligands with nucleic acids containing multiple binding sites are treated using the classical reaction‐diffusion equation applied to a spherical cell model of the nucleic acid solution and a diffuse‐sphere model for the nucleic acid chain molecule. Both uniform and Gaussian distributions of chain segments are analyzed. In general, the details of the segment distribution do not have a major effect on the kinetics of association. Domain effects are best examined experimentally by determining the effect of the molecular weight of the nucleic acid on the kinetics of the association reaction. A theoretical framework is presented that permits such data to be analyzed simply. Kinetic studies over a wide range of nucleic acid molecular weights are required in order to separate the contributions of diffusion and reaction to the observed kinetics, and to determine the contributions of site‐based and molecule‐based elements to the rate constants.
Thermodynamic parameters for the helix–coil thermal transition of ribonuclease‐S‐peptide and derivatives from 1H‐nmr data
Authors: Rico M. , Santoro J. , Bermejo F. J. , Herranz J. , Nieto J. L. , Gallego E. , Jiménez M. A. 
Published: December 2004

AbstractValues for the thermodynamic quantities, ΔH° = 11.8 ± 2.0 Kcal/mole and ΔS° = 43.6 ± 6.0 e.u., of the 3‐13 helix–coil equilibrium of isolated S‐peptide (19 residue N‐terminal fragment of ribonuclease A) in aqueous solution (3 m M, 1M NaCl, pD 5.4) have been determined from a joint analysis of the Thr 3γ, Ala 6β, Phe 8meta, and Phe 8para 1H chemical shift vs temperature curves (−7 to 80°C) in several aqueous–trifluorethanol mixtures. Chemical shifts in the coil and in the helix have been determined for up to 16 protons belonging to the 3‐13 fragment. Thermodynamic parameters have also been determined for C‐peptide (13 residue fragment) and a number of S‐peptide derivatives. From the variation of the values of the thermodynamic parameters at pD 2.5, 5.4, and 8.0, a quantitation of the two helix‐stabilizing side‐chain interactions can be made: (1) Δ(ΔH°) ≃ 5 Kcal/mole and Δ(ΔS°) ≃ 18 e.u. for the salt bridge Glu 2− … Arg 10+ and (2) Δ(ΔH°) ≃ 3 Kcal/mole and Δ(ΔS°) = 9 e.u. for the one in which the His 12+ imidazolium group is involved, presumably a partial stacking with the Phe 8 side chain.
Enantioselective interactions of inversion‐labile trigonal iron(II) complexes upon binding to DNA
Authors: Härd Torleif , Nordén Bengt 
Published: December 2004

AbstractWe studied the interactions of the substitution‐inert inversion‐labile complexes Fe(bipy) and Fe(phen) [and the inversion‐stable complex Ru(bipy)] with DNA. The association of these complexes to DNA is mainly electrostatic, and Fe(phen) shows a more effective binding to DNA than the two bipyridyl complexes, possibly owing to a different binding mode. The interactions are enantioselective, leading to a Pfeiffer shift in the diastereomeric inversion equilibria and an excess of the Δ‐enantiomer of Fe(phen) and Fe(bipy), which is directly monitorable through CD. The partition constants for the inversion equilibrium range from 1.3 to 2.0 for Fe(bipy) and Fe(phen), depending on ionic conditions. From flow LD information about the orientation of the complexes on DNA was obtained: it is consistent with a fit of the Δ‐enantiomer in the major groove of the right‐handed DNA helix. The mechanisms of interaction are discussed against equilibrium, spectroscopic, and kinetic data.
Analysis of the interaction of membrane‐active peptides with membranes: The case of melittin in surfactant assemblies
Authors: Chandani Bina , Balasubramanian D. 
Published: December 2004

AbstractSome of the factors that govern the interaction between membrane‐active peptides and membranes were analyzed using melittin as an example. The structural properties of melittin were studied in a variety of micellar and reverse micellar assemblies of varying sizes, shapes, and net charges. The roles of the polarity, packing, and the charge carried by the host assembly on the structural features of the incorporated melittin are delineated. Such an analysis is expected to be of relevance to other membrane‐active peptides as well.
Kinetics of ethidium's intercalation in packaged bacteriophage T7 DNA: Effects of DNA packing density
Authors: Griess Gary A. , Serwer Philip , Kaushal Varsha , Horowitz Paul M. 
Published: December 2004

AbstractThe kinetics of ethidium's intercalative binding to DNA packaged in bacteriophage T7 and two T7 deletion mutants have been determined, using enhancement of fluorescence to quantitate binding. At a constant ethidium concentration, the results can be described as first‐order binding with two different rate constants,k(=k1+k−1) andk(=k2+k−2). The larger rate constant (k) was at least four orders of magnitude smaller than the comparable first‐order forward rate constant for binding to DNA released from its capsid. At 25°C values ofkdecreased as the amount of DNA packaged per internal volume increased. This latter observation indicates that the rate of ethidium's binding to packaged T7 DNA is limited by an event that occurs inside of the DNA‐containing region of T7, not by the crossing of T7 capsid's outer shell. Arrhenius plots ofkMare biphasic, indicating a transition for packaged DNA at a temperature of 20°C. The data indicate thatks are limited by either sieving of ethidium during its passage through the packaged DNA or subsequent hindered intercalation.
Calculations on the effect of methylation on the electrostatic stability of the B‐ and Z‐conformers of DNA
Authors: Pack George R. , Prasad C. V. , Salafsky Joshua S. , Wong Linda 
Published: December 2004

AbstractThe three‐dimensional Poisson–Boltzmann equation for the distribution of counterion charge density around double‐helical DNA has been solved for solutions of .01M, .10M, and .20M monovalent salt. The polymers, poly[d(CpGp)] and poly[d(m5CpGp)], were studied in the B‐ and the Z‐conformations. The effect of methylation on the relative stabilities of these conformers in solutions of different ionic strengths is known to favor the Z‐form. Accumulation of charge density around the B‐ and the Z‐conformers is compared in detail. The relative electrostatic stabilities of the B‐ and Z‐conformers in .01M, .10M, and .20M solutions are compared and discussed in terms of the ion–DNA interactions and the self‐energy of the structured ionic environment. The ion–DNA interaction energies, termed “phosphate screening,” monotonically decrease with ionic strength and are consistent with a B‐to‐Z conformation change induced in either polymer by increased electrolyte concentration. However, these calculated energies alone do not account for the fact that the ionic strength at the midpoint of the transition of the methylated polymer is substantially lower than that of its unmethylated analogues. The phosphate screening effect is counterbalanced by changes in the self‐energy required for the creation of the structured counterion environment. This self‐energy of the electrolyte environment monotonically increases with ionic strength. Methylation‐induced shifts in the overall conformational equilibria depend on the relative changes of these competing effects. Increasing salt concentration is calcualted to favor the Z‐conformer. The effect of methylation, lowering the ionic strength of the transition midpoint, is proposed to originate in minor structural changes in the Z‐form of the polymer, making the groove more accessible to counterions in the G(3′ – 5′)C region. This allows a redistribution of counterion density and a lowering of the self‐energy of the ionic environment, conferring added stability to the Z‐conformation, as indicated by calculations of relative entropies. The experimentally observed temperature dependence of the B‐to‐Z transition, however, cannot be explained without assuming the release of bound water. Maps of the calculated three‐dimensional structure at the counterion distribution near the surface of these molecules in both the B‐ and the Z‐forms are also presented.
Sequence‐dependence of the CD of synthetic double‐stranded RNAs containing inosinate instead of guanylate subunits
Authors: Ratliff Robert L. , Liu Jung‐Jen , Vaughan Marilyn R. , Gray Donald M. 
Published: December 2004

AbstractThe CD spectra and melting profiles have been measured for nine synthetic double‐stranded RNAs containing I · C instead of G · C base pairs: poly[r(I) · r(C)], poly[r(I‐C) · r(I‐C)], poly[r(A‐I‐C) · r(I‐C‐U)], poly[r(A‐C) · r(I‐U)], poly[r(A‐I) · r(C‐U)], poly[r(A‐C‐C) · r(I‐I‐U)], poly[r(A‐A‐C) · r(I‐U‐U)], poly[r(A‐C‐U) · r(A‐I‐U)], and poly[r(A‐U‐C) · r(I‐A‐U)]. CD spectra have not previously been reported for the latter six of these polymers. The substitution of inosinate for guanylate led to recognizable CD differences, with all but two of the polymers having two resolved positive bands above 230 nm. Also, the I‐containing RNAs differed from their G‐containing counterparts in the almost complete absence of negative CD bands at long wavelengths and in the reduction of negative CD bands near 210 nm. First‐neighbor comparisons showed that the CD spectra of the I‐containing RNAs were consistent with the nearest‐neighbor sequences of the polymers, as previously shown for G‐containing RNAs (D. M. Gray, J.‐J. Liu, R. L. Ratliff, and F. S. Allen, Biopolymers (1981) 20, 1337–1382). Moreover, two of the first‐neighbor comparisons involved spectra of poly[r(A) · r(U)] and poly[r(I) · r(C)], polymers known to be in the A family of conformations in fibers (S. Arnott, D. W. L. Hukins, S. D. Dover, W. Fuller, and A. Hodgson, (1973) J. Mol. Biol. 81, 107–122). Thus, differences in the CD spectra of I‐ and G‐containing RNAs could be simply explained as resulting from differences in the hypoxanthine and guanine chromophores, without invoking differences in conformation. Finally, melting temperatures of the I‐containing RNAs were found to vary much less with base composition than do the melting temperatures of G‐containing RNAs, since A · U base pairs are closer to I · C than to G · C base pairs in stability.
The hinge‐bending mode of a lysozyme–inhibitor complex
Authors: Bruccoleri Robert E. , Karplus Martin , McCammon J. Andrew 
Published: December 2004

AbstractThe hinge‐bending mode of hen egg white lysozyme is studied by a constrained minimization technique. Results with and without a bound inhibitor, tri‐N‐acetyl‐glucosamine, are obtained. The frequency of the mode with the inhibitor is found to be 4.3 cm−1, in contrast to 3.0 cm−1 for the free enzyme. Also, the hinge‐bending angle with the lowest energy is shifted 10° towards a more closed cleft in the bound species. The main contribution to these differences arise from interactions with the residues lining the cleft and those on the back side of it. Structural details that account for the energetics are presented. The method of calculation is somewhat different from a previous study [J. A. McCammon, B. R. Gelin, M. Karplus & P. G. Wolynes, (1976) Nature 262, 325–326] to reduce the likelihood of artifacts in the results.