bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solution properties of sodium alginate
Authors: Mackie W. , Noy R. , Sellen D. B. 
Published: December 2004

AbstractSodium alginate fractions derived from three different sources—Laminaria hyperboria (75% guluronate), Fucus vesicularus (95% mannuronate), and Azotobacter vinelandii (85% mannuronate)—were investigated in aqueous solution over a wide range of ionic strength and pH using the techniques of light scattering, viscometry, and osmometry. Light‐scattering data extrapolated to infinite ionic strength yielded b0 = 4.7 ± 0.3 and 3.0 ± 0.2 nm for the unperturbed effective bond lengths of the guluronate‐ and mannuronate‐rich samples, respectively. These values are in the same ratio as predicted by conformational analysis, although lower by a factor of 0.7, probably due, in part at least, to the fact that measurements cannot be made on pure homopolymers. A comparison of the light‐scattering and the viscosity data indicated that Φ in the Flory‐Fox equation is lower than for more flexible polymers and increases with molecular weight, probably due to decreasing hydrodynamic permeability. Mark‐Houwink exponents obtained from data extrapolated to infinite ionic strength were found to be considerably greater than 0.5, and we attribute this entirely to a variation in Φ. Comparison of the results obtained for the two mannuronate‐rich samples indicated that the value of Φ and its variation with molecular weight can, in the case of alginates, differ markedly for chains, which, although having chemical differences, have similar chain statistics.
Helix–coil transitions in a simple polypeptide model
Authors: McCammon J. A. , Northrup S. H. , Karplus M. , Levy R. M. 
Published: December 2004

AbstractA simplified model of a polypeptide chain is described. Each residue is represented by a single interaction center. The energy of the chain and the force acting on each residue are given as a function of the residue coordinates. Terms to approximate the effect of solvent and the stabilization energy of helix formation are included. The model is used to study equilibrium and dynamical aspects of the helix–coil transition. The equilibrium properties examined include helix–coil equilibrium constants and their dependence on chain position. Dynamical properties are examined by a stochastic simulation of the Brownian motion of the chain in its solvent surroundings. Correlations in the motions of the residues are found to have an important influence on the helix–coil transition rates.
Kinetics of reactions involving DNA containing stress‐induced single‐stranded regions
Authors: Benham Craig J. 
Published: December 2004

AbstractThe theoretical kinetics are analyzed for reactions between torsionally stressed DNA and another compound which reacts at different rates with portions of the substrate molecule which are in different conformational states. These reactions are assumed to obey Michaelis‐Menten kinetics, so no cooperative effects occur. The DNA is regarded as being susceptible to a stress‐induced local conformational transition as described recently by Benham. Briefly, alterations in torsional stress consequent on superhelicity effectively change the relative concentrations of the two conformational states of the substrate, thereby influencing the course of the reaction. This theory is developed for transition between the B‐form helix and the single‐stranded, random‐coil states. To illustrate the influence of posited stress‐induced melting on kinetics, calculations are made on simple models of two biochemical phenomena. First, the variations in initial nicking rates of single‐strand‐specific endonucleases with substrate superhelicity are interpreted as arising from changes in the concentration of (stress‐induced) single‐stranded binding sites. Second, the observed dependence of the transcription rate of RNA polymerase core enzyme on substrate superhelicity is interpreted in terms of a model in which the rate‐limiting step in the initiation event is the formation of a complex between the enzyme and a single‐stranded region. Related experimental results are shown to be qualitatively consistent with the suggestion that sufficiently supercoiled DNA contains locally melted regions.
Effect of some organic cosolvents on the reaction of hemoglobin with oxygen
Authors: Cordone Lorenzo , Cupane Antonio , San Biagio Pier L. , Vitrano Eugenio 
Published: December 2004

AbstractWe studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod‐Wyman‐Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this constant.
Temperature dependence of the effects of some monohydric alcohols on the oxygen affinity of hemoglobin: Determination and analysis of thermodynamic parameters
Authors: Cordone Lorenzo , Cupane Antonio , San Biagio Pier L. , Vitrano Eugenio 
Published: December 2004

AbstractWe studied the effects of methanol, ethanol, iso‐propanol, and n‐propanol on the reaction of hemoglobin with oxygen at various temperatures. The analysis of the results in terms of the Monod‐Wyman‐Changeux model allowed determination of the overall contribution of the alcohols to the standard enthalpy and entropy differences between the T and R states of hemoglobin. A phenomenological approach allowed us to obtain separately the contributions related to the variations of the bulk dielectric constant of the solvent (bulk electrostatic contributions) and the contributions related to other effects (non‐bulk‐electrostatic contributions). The values of non‐bulk‐electrostatic contributions to ΔΔH and ΔΔS supported the suggestion that these contributions are mainly related to protein‐solvent hydrophobic interactions.
Conformation and dynamic structure of poly(inosinic acid) in neutral aqueous solution by 1H‐, 2H‐, 13C‐, and 31P‐NMR spectroscopy
Authors: Neumann J. M. , Tran‐Dinh S. 
Published: December 2004

AbstractThe conformation and dynamic structure of single‐stranded poly(inosinic acid), poly(I), in aqueous solution at neutral pH have been investigated by nmr of four nuclei at different frequencies: 1H (90 and 250 MHz), 2H (13.8 MHz), 13C (75.4 MHz), and 31P (36.4 and 111.6 MHz). Measurements of the proton‐proton coupling constants and of the 1H and 13C chemical shifts versus temperature show that the ribose is flexible and that base‐base stacking is not very significant for concentrations varying from 0.04 to 0.10M in the monomer unit. On the other hand, the proton T1 ratios between the sugar protons, T1 (H1′)/T1 (H3′), indicate a predominance of the anti orientation of the base around the glycosidic bond. The local motions of the ribose and the base were studied at different temperatures by measurements of nuclear Overhauser enhancement (NOE) of protonated carbons, the ratio of the proton relaxation times measured at two frequencies (90 and 250 MHz), and the deuterium quadrupolar transverse relaxation time T2. For a given temperature between 22 and 62°C, the 13C‐{1H} NOE value is practically the same for seven protonated carbons (C2, C8, C1′, C2′, C3′, C4′, C5′). This is also true for the T1 ratio of the corresponding protons. Thus, the motion of the ribose–base unit can be considered as isotropic and characterized by a single correlation time, τc, for all protons and carbons. The τc values determined from either the 13C‐{1H} NOE or proton T1 ratios, T1(90 MHz)/T1(250 MHz), and/or deuterium transverse relaxation time T2 agree well. The molecular motion of the sugar‐phosphate backbone (O‐P‐O) and the chemical‐shift anisotropy (CSA) were deduced from T1 (31P) and 31P‐{1H} NOE measurements at two frequencies. The CSA contribution to the phosphorus relaxation is about 12% at 36.4 MHz and 72% at 111.6 MHz, corresponding to a value of 118 ppm for the CSA (σ = σ∥ − σ⟂). Activation energies of 2–6 kcal/mol for the motion of the ribose–base unit and the sugarphosphate backbone were evaluated from the proton and phosphorus relaxation data.
Dynamic light‐scattering studies of internal motions in DNA. III. Evidence for titratable joints associated with bound polycations
Authors: Lin S. C. , Thomas J. C. , Allison S. A. , Schurr J. M. 
Published: December 2004

AbstractDynamic light‐scattering techniques are employed to study the internal Brownian motions of a commercial calf thymus DNA, clean and contaminated ϕ29 DNAs, and a clean ϕ29 DNA with bound spermidine as a function of pH. The Rouse‐Zimm model parameters of both calf thymus and contaminated ϕ29 DNAs differ substantially from those of clean ϕ29 DNA in the neutral‐pH region. However, this difference is largely removed by adding 0.01M EDTA (which has no effect on clean ϕ29 DNA) to the calf thymus DNA sample. These findings imply the existence in that preparation of polycation contaminants, presumably basic proteins, that can substantially alter the local mechanical properties of the DNA near their binding sites. The internal motion parameters kBT/f and b of both calf thymus and contaminated ϕ29 DNAs are found to exhibit pronounced characteristic variations between pH 8.5 and 10.5, over which range there is essentially no detectable titration to a resolution of about 1% of the base pairs. These variations, which are not observed for clean ϕ29 DNA, are qualitatively similar to those previously reported for a ϕ29 DNA with 21 single‐strand breaks per chain. This indicates the formation of titratable joints associated with bound polycation contaminants. These basic ligands presumably facilitate local denaturation by stabilizing the titration of one or more protons on base‐ring nitrogens near their binding sites. Spermidine binding up to 85–87% of neutralization of the total DNA charge has only a relatively minor effect on the internal motion parameters at neutral pH in 0.01M NaCl. However on raising the pH to 10.2, the internal motion parameter kBT/f undergoes a marked decrease similar to that observed for both calf thymus and contaminated ϕ29 DNAs and also ϕ29 DNA with single‐strand breaks. This indicates that spermidine, too, is capable of inducing titratable joints. Evidence is presented that the titratable joints associated with bound polycations on the calf thymus DNA may serve primarily as torsion joints, as was found previously for the titratable joints associated with single‐strand breaks.
Theoretical π‐π* circular dichroic spectra of helical poly(glycine) and poly(L‐alanine) as functions of backbone torsion angles
Authors: Applequist Jon 
Published: December 2004

AbstractCircular dichroic spectra and oscillator strengths of the π‐π transition near 190 nm are calculated for helical (Gly)6 and (Ala)6 at 30° intervals of the backbone torsion angles (ϕ,ψ) over the range ‐180° ≤ ϕ ≤ ‐60°, −60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)6 at (ϕ,ψ) angles corresponding to the α‐helix, the poly(Pro) II helix, a collagen single helix, a poly‐(MeAla) helix, and single β‐helices are found to agree well with most of the available experimental data.
Electric birefringence of restriction enzyme fragments of DNA: Optical factor and electric polarizability as a function of molecular weight
Authors: Stellwagen Nancy C. 
Published: December 2004

AbstractThe electric birefringence of restriction enzyme fragments of DNA has been investigated as a function of DNA concentration, buffer concentration, and molecular weight, covering a molecular weight range from 80 to 4364 base pairs (bp) (6 × 104–3 × 106 daltons). The specific birefringence of the DNA fragments is independent of DNA concentration below 20 μg DNA/ml, but decreases with increasing buffer concentration, or conductivity, of the solvent. At sufficiently low field strengths, the Kerr law is obeyed for all fragments. The electric field at which the Kerr law ends is inversely proportional to molecular weight. In the Kerr law region the rise of the birefringence is accurately symmetrical with the decay for fragments ≤ 389 bp, indicating an induced dipole orientation mechanism. The optical factor calculated from a 1/E extrapolation of the high field birefringence data is −0.028, independent of molecular weight; if a 1/E2 extrapolation is used, the optical factor is −0.023. The induced polarizability, calculated from the Kerr constant and the optical factor, is proportional to the square of the length of the DNA fragments, and inversely proportional to temperature. Saturation curves for DNA fragments ≤ 161 bp can be described by theoretical saturation curves for induced dipole orientation. The saturation curves of larger fragments are broadened, because of a polarization term which is approximately linear in E, possibly related to the saturation of the induced dipole in high electric fields. This “saturated induced dipole” is found to be 6400 D, independent of molecular weight. The melting temperature of a 216‐bp sample is decreased 6°C in an electric field of 8 kV/cm, because the lower charge density of the coil form of DNA makes it more stable in an electric field than the helix form.
Structure of viral φ29 DNA condensed by simple triamines: A light‐scattering and electron‐microscopy study
Authors: Allison Stuart A. , Herr John C. , Schurr J. Michael 
Published: December 2004

AbstractThe structures of viral φ29 DNA condensed by triamines, principally spermidine, in 10−3M NaCl were investigated by static and dynamic light scattering and electron microscopy. All of the results for DNA condensed in 30 μM spermidine at neutral pH are quantitatively consistent with a toroidal structure with a mean outer diameter of 1850 Å. At pH 10.2, however, condensed structures of a completely different size and shape are observed for the first time. These structures are also more irregular in shape and more polydisperse than those at neutral pH. This conformational change is believed to result from a change in the mode of spermidine binding that is coupled to, or associated with, the (premature) titration of protons on the base‐ring nitrogens of guanine and thymine. Besides spermidine, certain homologs of spermidine, in which the butyl moiety of spermidine was replaced by longer pentyl through octyl moieties, were also studied. Though all of the triamines condensed the DNA at 30 μM, aggregation became a more prevalent occurrence as the length of the end chain increased. This suggests that crosslinking may play an important role in the condensation process. Finally, these aggregates are dissociated to a considerable extent at pH 10.2, and the resulting compact structures appear to be quite similar, independent of the triamine used to condense the DNA. The observed partial breakdown of aggregates is also consistent with the hypothesis of a change in mode of triamine binding at pH 10.2.
Acoustic modes and nonbonded interactions of the double helix
Authors: Mei W. N. , Kohli M. , Prohofsky E. W. , Van Zandt L. L. 
Published: December 2004

AbstractObservations of acoustic velocities in DNA fibers have been used to refine nonbonded force constants for the DNA double helix. Long‐range forces are found to be needed for A conformation and are likely to dominate in B conformation as well. The acoustic dispersion curves are described and calculated. A correction due to the effects of water is calculated. The effect of nonbonded interaction on other vibrational modes is calculated.
Locations of frequently opening regions on natural DNAs and their relation to functional loci
Authors: Gotoh Osamu , Tagashira Yusaku 
Published: December 2004

AbstractThe probability of each base pair being in open state under premelting conditions was calculated and plotted against the base number for nine DNA genomes whose entire nucleotide sequences have been determined. The base‐pair opening profiles thus obtained were compared with the functional maps. Origins of DNA replication fall on frequently opening regions for five of six DNA genomes with known initiation sites of replication. Coincidence of frequently opening regions with promoters and terminators of transcription is most prominent for DNAs with block heterogeneity in sequence such as papovavirus DNAs, a Colicin El‐related plasmid pAO3, pBR322, and Transposon 3 (Tn 3) DNAs, while this coincidence is less apparent in DNAs with random sequence such as the replicative form of ϕX174 and G4 phage DNAs. In fd phage DNA, about half the promoters are located in frequently opening regions, although the strength of a promoter is not correlated with the frequency of opening of base pairs. Correlation of frequently opening regions and gene boundaries is not so obvious as claimed previously. As a whole, coincidence of functional loci and frequently opening regions defined in base‐pair opening profiles is far from perfect but much better than that previously inferred from the conventional running average of local A + T content, theoretical denaturation mapping, or electron microscopy of partially denatured DNA molecules.
Does perchlorate ion change A·U combining ratios?
Authors: Howard Frank B. , Roy Kunal B. , Frazier Joe , Miles H. Todd 
Published: December 2004

AbstractInfrared spectroscopy and equilibrium binding studies have been used to determine the combining ratio of adenosine and poly(U) in 1M NaClO4 solution. In contrast to a recent report, we find exclusively 1:2 stoichiometry in this solvent. Ultraviolet and infrared spectroscopy have been employed to show that the stoichiometry of poly(A) interaction with poly(U) is unaffected by 1M NaClO4.
Kinetics of chemical modification of arginine and lysine residues in calf thymus histone H1
Authors: Mita Kazuei , Ichimura Sachiko , Zama Mitsuo , Hamana Koei 
Published: December 2004

AbstractThe arginine and lysine residues of calf thymus histone H1 were modified with large molar excesses of 2,3‐butanedione and O‐methylisourea, respectively. Kinetic study of the modification reaction of the arginine residue revealed that the reaction is divided into the two pseudo‐first‐order processes. About a third (1 Arg) of the total arginine residues of the H1 molecule was rapidly modified without causing any detectable structural change of the molecule, and the slow modification of the remaining arginine residues (2 Arg) led to a loss of the folded structure of H1. In the case of lysine residue modification, 93% (56 Lys) of the total lysine residues of the H1 was modified with the same rate constant, while 7% (4 Lys) of lysine residue remained unmodified. When the reaction was performed in the presence of 6M guanidine‐HCl, all of lysine residues were modified. It is concluded that the 2 arginine and 4 lysine residues resistant to modification are buried in interior regions of the H1 molecule and play an important role in the formation of the H1 globular structure, while the other 1 arginine and 56 lysine residues are exposed to solvent.
Ionic strength effects on macroion diffusion and excess light‐scattering intensities of short DNA rods
Authors: Fulmer Andrew W. , Benbasat Julyet A. , Bloomfield Victor A. 
Published: December 2004

AbstractQuasielastic and static light‐scattering measurements were made on DNA isolated from chicken erythrocyte mononucleosomes as a function of ionic strength between 6 × 10−4 and 1.0M. A transition from single‐exponential autocorrelation functions to markedly non‐single‐exponential decays was observed around 10−2M ionic strength and was accompanied by a large decrease in the excess light‐scattering intensity. Autocorrelation functions recorded below 10−2M salt were well fit by the sum of two exponential relaxation which differed by as much as 100‐fold in time constants. Apparent diffusion coefficients for the fast and slow processes plateaued around 10−3M with numerical values approximately 10‐fold and 1/10, respectively, of the translational diffusion coefficient for mononucleosome DNA at high ionic strength. This behavior is similar to that observed with poly(L‐lysine), for which the slow decay has been associated with a transition to an extraordinary phase. The strong and complex salt dependence observed here illustrates potential difficulties in deriving structural information from scattering by polyions at low ionic strength.
Elastin as a random‐network elastomer: A mechanical and optical analysis of single elastin fibers
Authors: Aaron B. B. , Gosline J. M. 
Published: December 2004

AbstractThe physical properties of single, 5–8‐μm diameter, water‐swollen elastin fibers have been investigated on a microtest apparatus attached to a polarizing microscope. Analysis of the mechanical and optical properties at extensions below 100% indicate that the elastic modulus (G) has a value of 4.1 × 105 N m−2, the average molecular weight of chains between crosslinks is in the range of 6000–7100, and the stress optical coefficient (C′) is 1 × 10−9 m2 N−1 at 24°C. Analysis of the temperature dependence of the stress optical coefficient indicates that the polarizability of the random link decreases with increasing temperature, with an apparent activation energy for this process of the order of 1.6 kcal/mol. Analysis of the non‐Gaussian mechanical and optical properties at extensions above about 100% suggest that the chains between crosslinks contain approximately 10 “effective” random links, with each link consisting of 7–8 amino acid residues. These parameters for the random chains in the elastin network have been used to predict the dimensions of other random proteins. The close correlation of these predictions with published values for the dimensions of a series of proteins in solution in 6M guanidinium hydrochloride provides an independent test of the appropriateness of our analysis.
The possibility of intrinsic local curvature in DNA toroids
Authors: Manning Gerald S. 
Published: December 2004

AbstractA variety of solution conditions are known to induce collapse of linear DNA into a compact configuration without dramatic change of local structure. When visualized, these compact forms frequently have a toroidal appearance. We ask whether the molecular basis of the toroidal shape can be a stable curvature of isolated rodlike DNA segments. Application of the classical Euler‐Lagrange theory for the buckling of elastic rods provides us with an affirmative answer. Specifically, we see that, in principle, sufficient addition of inert polymer to DNA solutions can induce buckling of DNA segments. However, no attempt is made to quantitate the Euler‐Lagrange condition for sufficiency in terms of added polymer concentration. We find also that complete neutralization of the phosphate charge is more than sufficient to induce buckling of DNA segments of length comparable to a Kuhn segment. The quantitative argument involves comparison of buckling forces provided by polyelectrolyte theory with the Euler‐Lagrange criterion. Knowledge of the ionic‐strength dependence of DNA bending stiffness (persistence length) is not required.