bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apparent persistence lengths and diffusion behavior of high molecular weight hyaluronate
Authors: Ghosh Snehasish , Li Xiao , Reed Christopher E. , Reed Wayne F. 
Published: December 2004

AbstractHigh purity, high molecular weight hyaluronate from bacteria and rooster comb exhibited clear polyelectrolyte properties, as observed by static and dynamic light scattering. The scattered intensity of hyaluronate solutions increased markedly with ionic strength, while the radii of gyration decreased. Apparent persistence lengths within the wormlike chain model in the coil limit were estimated as a function of ionic strength. The total apparent persistence length varied from about 87 Å in the high ionic strength limit to nearly 400 Å at 1 mM added NaCl. The apparent electrostatic persistence length varied approximately as the inverse square root of the ionic strength. Deviations from the theoretically predicted inverse ionic strength dependence were investigated in terms of excluded volume effects. Dynamic light scattering yielded “ordinary phase” diffusion coefficients whose dependence on polymer and salt concentration agreed reasonably well with hydrodynamic coupled mode theory in the linear limit. Extrapolations to infinite polymer dilution at fixed salts yielded, surprisingly, a constant diffusion coefficient. Thus, there was no evidence of either polyion expansion or electrolyte friction effects in the infinite dilution diffusion coefficients. Since clear evidence for polyion expansion was seen in the static scattering, it is thought that the relative stiffness and consequent openness of the hyaluronate coils lead to partial free draining behavior. There was no evidence for an “extraordinary phase” under no added salt and low added salt conditions. The overall results are contrasted with the very different behavior previously reported for medium purity hyaluronate from animal sources.
A general secular equation for cooperative binding of n‐mer ligands to a one‐dimensional lattice
Authors: Chen Yi‐Der 
Published: December 2004

AbstractThe binding of n‐mer ligands to a one‐dimensional lattice involving many ligand species and complex multiple‐binding mechanisms is studied. We show that, when derived using the sequence‐generating function method of Lifson, the secular equation of any binding system with a finite number of “elementary units” can be expressed in a matrix determinant form that is very symmetric and easy to construct. In other words, for any binding system whose elementary units are known, the secular equation of the system can be obtained readily without going through the formal derivation of the equation. We also show that the “determinant” secular equation obtained using the present procedure can be employed directly to the calculation of binding isotherms.
Determination of the conformation of Lewis blood group oligosaccharides by simulation of two‐dimensional nuclear overhauser data
Authors: Cagas Perseveranda , Bush C. Allen 
Published: December 2004

AbstractThrough control of both the nmr probe temperature and of the solvent viscosity, phase‐sensitive two‐dimensional 1H nuclear Overhauser data (NOESY) at 300 and 500 MHz are obtained with excellent signal‐to‐noise ratios for Lewis blood group penta‐ and hexasaccharides isolated from human milk. Relatively long mixing times are required to produce measurable NOE intensities in these oligosaccharides, which makes a full relaxation maxtrix analysis necessary. By measurements of selective T1 for a few isolated 1H resonances, it was possible to generate a simulation of the complete NOESY spectrum at arbitrary mixing time for comparison with the experimental data. From an exhaustive search of the conformational space, it was found that only a small range of glycosidic dihedral angles for the nonreducing terminal Lewis blood group determinant fragments of the milk oligosaccharides LNF‐2 and LND‐1 produce simulated spectra agreeing within experimental error to the data. Conformational energy calculations reveal that each of these conformations is also one of minimum energy. It is concluded that the Lewisa and Lewisb oligosaccharides adopt relatively compact rigid structures in solution, as shown by the observation of cross peaks between protons in nonadjacent residues. Like the blood group A and H oligosaccharides, there exists only a small dependence of the conformation for Lewisa and Lewisb oligosaccharides on solvent. The apparent lack of dependence of conformation of these oligosaccharides on DMSO in D2O suggests that modification of solvent viscosity with mixtures of DMSO : D2O may provide a useful general strategy of NOESY studies of oligosaccharides.
The reliability of wormlike polysaccharide chain dimensions estimated from electron micrographs
Authors: Stokke Bjørn T. , Brant David A. 
Published: December 2004

AbstractElectron micrographs of alginate, xylinan, xanthan, and scleroglucan were prepared by vacuum‐drying aqueous glycerol‐containing solutions, and then heavy‐metal, low‐angle rotary replicated. Quantitative methods for excluding streamlining effects and deformation artifacts were developed and applied to the digitized polymer contours prior to analysis of stiffness. The apparent macromolecular dimensionalities were not obtainable on the basis of the change in the scaling coefficient a relating the rms end‐to‐end distance and the contour length, 〈r2〉1/2 ∼ Lα, for chains subject to the excluded volume effect in two and three dimensions. Using a two‐dimensional model, the persistence length of these molecules was estimated to be (9 ± 1) nm (alginate), (25 ± 4) nm (xylinan), (30 ± 4) nm (single‐stranded xanthan), (68 ± 7) nm (double‐stranded xanthan), and (80 ± 10) nm (scleroglucan). Monte Carlo calculations for wormlike chains close to an interacting surface or confined to the region between two surfaces showed that (1) strongly adsorbed molecules are essentially two‐dimensional and (2) molecules restricted to the space between two surfaces separated by a distance less than 20% of the persistence length are two‐dimensional in their directional correlation. The somewhat low estimates of the persistence lengths obtained from the electron micrographs compared with those reported from solution measurements can be accounted for by the adoption of a strictly two‐dimensional model in the analysis, whereas the adsorbed polymers are most likely intermediate between the two‐and three‐dimensional cases. The model calculations and the analysis of the electron micrographs suggest that stiffness parameters are obtainable from the electron micrographs when the proper theoretical description are used in the analysis.
On the kinetics of oligomer binding
Authors: Poland Douglas 
Published: December 2004

AbstractThe kinetics of oligomer binding to a polymer are treated in the approximation that the internal states of the oligomer–polymer complex equilibrate rapidly compared with the rate of binding. In that case one can use equilibrium statistical mechanics to give the density of appropriate binding sites required in the kinetic equation. In this manner one can obtain a general differential equation in one variable (the net density of oligomer bound) for the case of cooperative binding. Several simple, but accurate, approximate solutions to the binding kinetics are presented.
Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. I. Spectral parameters of amino acid residue absorption bands
Authors: Venyaminov S. Yu. , Kalnin N. N. 
Published: December 2004

AbstractInfrared spectra of the amino acid residues in H2O solution have been obtained in the 1800–1400‐cm−1 region. It has been established that amino acid residues of arginine, asparagine, glutamine, aspartic and glutamic acids, lysine, tyrosine, histidine, and phenylalanine have intensive absorption in this spectral region. Infrared spectra for a set of model compounds have been measured. On the basis of these data, spectral parameters of amino acid residue absorption bands have been determined.
Variation of the permeability of bacteriophage T4: Analysis by use of a protein‐specific probe for the T4 interior
Authors: Griess Gary A. , Khan Saeed A. , Serwer Philip 
Published: December 2004

AbstractThe permeability of bacteriophage T4 and the change in T4 permeability caused by mutation to osmotic shock resistance are investigated here by quantification of the kinetics with which both a DNA‐specific probe (ethidium) and a protein‐specific probe [1,1′‐bi(4‐anilino) naphthalene‐5,5′‐di‐sulfonic acid, or bis‐ANS] bind to T4. In the case of an osmotic shock‐resistant mutant, T40s41, both ethidium and bis‐ANS bind with first order kinetics. The first‐order rate constant (k*) for both bis‐ANS and ethidium is a function of anion type and concentration. Adenosine triphosphate, phosphate, bisulfite, sulfate, and acetate anions all reduce k* below the k* observed when chloride is the only anion. When chloride is the only anion at 25°C, k* values for binding to T40s41 are orders of magnitude above k* values for binding to wild‐type T4 (T4wt). At 25°C, k* forT4wt is too small to measure, but k* for T4wt increases at 50–55°C to values approaching those measured for T40s41, without inactivating T4wt, when chloride is the only anion; during heating, T4wt is stabilized by both ethidium and bis‐ANS. Binding to T4wt is reversible at 50‐55°C, but not at 25°C. Equilibrium binding of bis‐ANS to T40s41 reveals 112 ± 24 sites per T4 capsid. Equilibrium binding of ethidium to T40s41 reveals both high‐ and low‐affinity sites previously observed in the packaged DNA of other bacteriophages. The ATP‐induced decrease in k* is not accompanied by a decrease in equilibrium binding. The following hypotheses are presented to explain the above data: (a) All detected bis‐ANS binding sites on T4 are interior to the outer surface of T4. (b) The value of k* for both bis‐ANS and ethidium is controlled at the port(s) of passage through the outer shell of the T4 capsid. (c) The anions present control k* values at the port(s) of entry, probably by controlling the size of this port. The effects on k* of phosphate explain the otherwise paradoxical observation [P. J. McCall and V. A. Bloomfield (1976) Biopolymers 15, 2323–2336] that in a phosphate buffer the permeabilities of T4wt and T40s41 are the same.
L‐Alanyl‐L‐alanyl‐L‐alanine: Parallel pleated sheet arrangement in unhydrated crystal structure, and comparisons with the antiparallel sheet structure
Authors: Hempel A. , Camerman N. , Camerman A. 
Published: December 2004

AbstractThe tripeptide L‐alanyl‐L‐alanyl‐L‐alanine has been crystallized from a water/dimethyl‐formamide solution in an unhydrated form, with cell dimensions a = 11.849, b = 10.004, c = 9.862 Å, β = 101.30°, monoclinic space group P21, with 4 molecules per cell (2 independent molecules in the asymmetric unit). The Structure was determined by direct methods and refined to a discrepancy index R = 0.057. The tri‐L‐alanine molecules are packed in a parallel pleated sheet arrangement with unusually long amide nitrogen‐carbonyl oxygen contacts within sheets. Comparisons are made with the antiparallel pleated sheet structure of tri‐L‐alanine hemihydrate, previously crystallized from the same solvent system.
Thermodynamics of drug–DNA interactions: Entropy‐driven intercalation and enthalpy‐driven outside binding in the ellipticine series
Authors: Schwaller Marc‐Antoine , Dodin Guy , Aubard Jean 
Published: December 2004

AbstractViscosimetric and kinetic results allow one to characterize three modes of DNA binding in the ellipticine series: (1) Ellipticine and its 9 methoxy derivative, which present maximal DNA lengthening properties and bind DNA through a single step mechanism, can be considered as pure intercalators. (2) Ellipticinium derivatives and short‐chain substituted oxazolopyridocarbazoles, which present intermediate DNA lengthening properties, bind DNA through a two‐step mechanism, one being intercalation. (3) Long‐chain substituted oxazolopyridocarbazole derivatives, which display the smallest DNA lengthening properties, bind DNA through a single‐step mechanism, probably resulting from an outside binding mode.The viscosimetric and kinetic results are compared with the thermodynamic results obtained from the temperature dependence of the binding constants. It appears that drugs binding on the outside of the DNA double helix tend to have large enthalpy and small entropy contributions, whereas pure intercalating drugs have contributions from both enthalpy and entropy, with entropy dominating by about 2 : 1. Drugs showing two binding modes exhibit a continuum between the aforementioned extremes, with no breaks in behavior.From this comparison, a correlation between thermodynamic data and DNA binding modes is proposed. Possible molecular implications of both enthalpy and entropy to DNA binding free energy are discussed.
Structure and antigenic activity of rubella E1 glycoprotein synthetic peptides
Authors: Neri P. , Corti M. , Lozzi L. , Valensin P. E. 
Published: December 2004

AbstractMinimal sequences of rubella E1 glycoprotein epitopes were previously identified as the tripeptide 250PER252 for the EP2 epitope, the tetrapeptide 260ADDP263 for the EP3 epitope, and the tripeptide 273EVW275 plus the octapeptide 278PVIGSQAR285 for the EP1 epitope.In order to establish for each epitope the shortest sequence that was able to give the maximum binding with human antirubella immunoglobulins, synthetic peptides with increasing number of residues flanking these essential parts of rubella E1 glycoprotein epitopes were synthesized and examined for their antigenic activity.Usually higher activity was observed with progressively longer homologues, whereas the additions of Pro‐271, Pro‐278 to 272GEVWVT277 peptide, and additions of Ala‐248 to 249TPERP253and 249TPERPR254, led to an abrupt decrease in binding. Taken together, our results indicated that the antigenic activity of the whole antigen could be dissected and reproduced using synthetic peptides of appropriate structure for each epitope.
Preferred conformation of peptides from Cα,α‐symmetrically disubstituted glycines: Aromatic residues
Authors: Crisma M. , Valle G. , Bonora G. M. , Toniolo C. , Lelj F. , Barone V. , Fraternall F. , Hardy P. M. , Maia H. L. S. 
Published: December 2004

AbstractThe conformational preference of Cα,α‐diphenylglycinc (Døg) and Cα,α‐dibenzylglycine (Dbz) residues was assessed in selected derivatives and small peptides by conformational energy computations, ir absorption, 1H‐nmr, and x‐ray diffraction. Conformational energy computations on the two monopeptides strongly support the view that these Cα,α‐symmetrically disubstituted glycines are conformationally restricted and that their minimum energy conformation falls in the fully extended (C5) region. The results of the theoretical analyses appear to be in agreement with the solution and crystal‐state structural propensities of three derivatives and seven di‐and tripeptides.
The kinetics of chain exchange in two‐chain coiled coils: αα‐ and ββ‐tropomyosin
Authors: Ozeki Sumio , Kato Tadashi , Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractMeasurements are presented on the time course of chain exchange among two‐chain α‐helical coiled coils of rabbit tropomyosin. All experiments are in a regime (temperature, protein concentration) in which coiled‐coil dimers are the predominant species. Self‐exchange in αα‐tropomyosin was investigated by mixing αα species with α*α*, the asterisk designating an α‐chain whose lone sulfhydryl (C190) has been blocked by carboxyamidomethylation. The overall process αα + α*α* ⇄ 2αα* is followed by measurement of the fraction (h ) of αα* species as a function of time. Similarly, self‐exchange in ββ‐tropomyosin is examined by measurements of the overall process: ββ + β*β* ⇄ 2ββ*, in which β* signifies a β‐chain blocked at both sulfhydryls (C36 and C190). The observed time course for both chains is well fit by the first‐order equation: h (t ) = h (∞)(1 − e), with h (∞) ≃ 0.5. This long‐time limit is as expected for self‐exchange, and agrees with experiments that attain equilibrium after slow cooling of thermally dissociated and unfolded chains. The simplest consonant mechanism is chain exchange by rate‐limiting dissociation of dimers followed by random reassociation. Kinetic analysis shows k 1 to be the rate constant for the chain dissociation step, a quantity not previously measured for any coiled coil. This rate constant for ββ species is about an order of magnitude greater than for αα. In both, the activation enthalpy and entropy are very large, suggesting that activation to an extensively (>50%) unfolded species necessarily precedes dissociation. Experiments are also reported for overall processes: αα + β*β* ⇄ 2αβ* and α*α* + ββ ⇄ 2α*β. Results are independent of which chain is blocked. Again h (∞) ≃ 0.5, in agreement with equilibrium experiments, and the time course is first order. The rate constants and activation parameters are intermediate between those for self‐exchange.
The hydration response of poly(L‐lysine) dynamics measured by 13C‐nmr spectroscopy
Authors: Swanson Scott D. , Bryant Robert G. 
Published: December 2004

Abstract13C‐nmr measurements are reported for samples of poly (L‐lysine) both static and spinning at the magic angle in the β‐sheet form as a function of water content. The addition of water decreases the side‐chain line widths considerably. Measurements of the cross‐polarization time constants indicate that hydration by either H2O or D2O increases the time constant. Measurements of spin–lattice relaxation times in the laboratory frame and the rotating frame indicate that hydration does not change the dynamics of the backbone carbon atoms in the β‐sheet structure appreciably, but the side‐chain atoms experience considerable increase in local mobility with increasing hydration. Deuteration of the exchangeable protons or the water has only small effects on the carbon relaxation times indicating that relaxation is driven by intramolecular dipole–dipole interactions.
Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules
Authors: Lee B. 
Published: December 2004

AbstractThe experimental thermodynamic data for the dissolution of five simple hydrocarbon molecules in water were combined with the solute–solvent interaction energy from a computer simulation study to yield data on the enthalpy change of solvent reorganization. Similar data were generated for dissolving these same solute molecules in their respective neat solvents using the equilibrium vapor pressure and the heat of vaporization data for the pure liquid. The enthalpy and the free energy changes upon cavity formation were also estimated using the temperature dependence of the solute–solvent interaction energy. Both the enthalpy and TΔS for cavity formation rapidly increase with temperature in both solvent types, and the free energy of cavity formation can be reproduced accurately by the scaled particle theory over the entire temperature range in all cases. These results indicate that the characteristic structure formation around an inert solute molecule in water produces compensating changes in enthalpy and entropy, and that the hydrophobicity arises mainly from the difference in the excluded volume effect.
Interaction of La(III) and Tb(III) ions with purine nucleotides: Evidence for metal chelation (N‐7‐M‐PO3) and the effect of macrochelate formation on the nucleotide sugar conformation
Authors: Tajmir‐Riahi Heidar‐Ali 
Published: December 2004

AbstractThe interaction of the La(III) and Tb(III) ions with adenosine‐5′‐monophosphate (5′‐AMP), guanosine‐5′‐monophosphate (5′‐GMP), and 2′‐deoxyguanosine‐5′‐monophosphate (5′‐dGMP) anions with metal/nucleotide ratios of 1 and 2 has been studied in aqueous solution in acidic and neutral pHs. The solid complexes were isolated and characterized by Fourier transform ir and 1H‐nmr spectroscopy.The lanthanide(III)–nucleotide complexes are polymeric in nature both in the solid and aqueous solutions. In the metal‐nucleotide complexes isolated from acidic solution, the nucleotide binding is via the phosphate group (inner sphere) and an indirect metal‐N‐7 interaction (outer‐sphere) with the adenine N‐1 site protonated. In the complexes obtained from neutral solution, metal chelation through the N‐7 and the PO group is prevailing. In aqueous solution, an equilibrium between the inner and outer sphere metal‐nucleotide interaction has been observed. The ribose moiety shows C2′‐endo/anti pucker in the free AMP anion and in the lanthanide(III)–AMP complexes, whereas the GMP anion with C2′‐endo/anti sugar conformation exhibits a mixture of the C2′‐endo/anti and C3′‐endo/anti sugar puckers in the lanthanide(III)–GMP salts. The deoxyribose has O4′‐endo/anti sugar pucker in the free dGMP anion and a C3′‐endo/anti, in the lanthanide (III)–dGMP complexes.
Experimental and theoretical studies of DNA separations by capillary electrophoresis in entangled polymer solutions
Authors: Grossman Paul D. , Soane David S. 
Published: December 2004

AbstractStudies of electrophoretic separations of DNA restriction fragments by capillary electrophoresis in solutions of (hydroxyethyl) cellulose (HEC) were performed. Rheological studies were used to confirm that the entanglement threshold (Φ*) for the HEC solutions used is approximately 0.004 g/mL, in good agreement with theoretical predictions. A mesh size an order of magnitude smaller than that found in agarose gels (on a per weight basis) was calculated using polymer‐entanglement theory and was confirmed by electrophoretic measurements. Electrophoretic migration was shown to follow the Ogston regime under most conditions. An approach for obtaining smaller mesh sizes is presented.
Structural properties of polydisperse biopolymer solutions: A light scattering study of bovine α‐crystallin
Authors: Schurtenberger P. , Augusteyn R. C. 
Published: December 2004

AbstractWe have measured 〈RH〉z, 〈R〉, and 〈M〉w for individual fractions of the protein α‐crystallin obtained by gel filtration of bovine lens nuclear extracts. A strong and monotonic decrease of 〈RH〉z and 〈M〉w with increasing elution volume could be observed, indicating a broad size distribution. The experimental results are quantitatively consistent with a polymerization of monomeric units into linear chains, which may have a certain degree of flexibility. Using theoretical expressions for 〈R〉 and RH originally derived for semiflexible polymers in solution, we can self‐consistently analyse the data from static and dynamic light scattering, and from electron microscopy experiments. We thus obtain detailed information on the molecular weight distribution and the quaternary structure of α‐crystallin in these solutions.