bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type I Collagen Fibrillogenesis: Initiation via Reversible Linear and Lateral Growth Steps
Authors: Silver F. H. , Langley K. H. , Trelstad R. L. 
Published: December 2004

AbstractType I collagen fibrillogenesis in vitro has been studied by laser light scattering, and the results indicate that initiation of aggregation involves at least two steps. Step I of aggregation involves no change in the intensity of scattered light at an angle of 90° and is accompanied by a decrease in the diffusion coefficient. Step II is characterized by an increased intensity of scattered light and decreased diffusion coefficients. Theoretical calculations using the Stokes‐Einstein equation for the translational diffusion coefficient and the Perrin equation for the frictional coefficient of a prolate ellipsoid indicate that the step I aggregates are 4D staggered linear dimers and trimers 570 and 845 nm long, whereas step II aggregates are greater than 950 nm in length. These dimensions are similar to those previously reported based on physicochemical measurements and electron microscopy. It is proposed that the rate and extent of fibrillogenesis in vitro is controlled by the concentration of the linear aggregates and that the effects of temperature and collagen concentration on fibrillogenesis previously observed are qualitatively explained in terms of their effects on the concentration of these aggregates.
Conformational difference in cation complexes of tetranactin in solution
Authors: Ueno Masaharu , Kyogoku Yoshimasa 
Published: December 2004

AbstractThe conformational changes and binding behavior of tetranactin on complexation with sodium, potassium, rubidium, cesium, and ammonium ions were investigated by the measurements of proton magnetic resonance, ir, and Raman spectra. It has been clearly shown that alkali cations coordinate to the oxygen atoms of both the carbonyl group and the tetra‐hydrofuran ring, but the ammonium ion coordinates only to the oxygen atom of the tetrahydrofuran. Among the alkali cations the potassium ion most strongly coordinates to the tetrahydrofuran oxygen atoms. The complexation with larger cations induces an expansion of the cavity of the macrocyclic ring of tetranactin and smaller cations contract the cavity. The evidence is revealed by the coupling constants of the methylene protons and the frequency separation between the carbonyl stretching vibrations of the ir‐ and Raman‐active modes. The conformations of the cation complexes in the solid are maintained in solution but that of the cation free form is not.
Characterization of meningococcal polysaccharides by light‐scattering spectroscopy. IV. Molecular weight distribution of group B meningococcal polysaccharide in buffer solution
Authors: Gulari Esin , Chu B. , Liu T. Y. 
Published: December 2004

AbstractWe report the first characterization of group B meningococcal polysaccharide at 28°C in 0.4M KCl and 0.05M sodium acetate at pH 5.61 and in pure water by means of light‐scattering spectroscopy. In buffer solution, the weight‐average molecular weight Mr = 1.46 × 105 g/mol, the Z‐average radius of gyration 〈rg2〉z1/2 = 26.3 nm, the second virial coefficient A2 = (2.12 ± 0.17) × 10−4 cm3 mol/g2, and the second virial coefficient of the diffusion expansion kD ≈ 79 g/g. By using a histogram approximation on the correlation function profile analysis, we observed size fractions of two sizes with rhL/rhS = 298 Å/50 Å and AL/AS = 82/18, where rh and A are the respective effective hydrodynamic radius and the integrated intensity and the subscripts L and S denote the large and small size fractions. In pure water, rhL/rhS = 402 Å/29 Å with AL/AS = 84/16. The linewidth results are consistent with the measurements on the angular distribution of scattered intensity. Furthermore, if we take the large fraction to behave more like solid spheres, we are able to determine a molecular weight distribution of B‐polysaccharide in buffer solution in a bimodal size distribution function.
Density gradient proportionality constants, density distributions, and pressure effects for three salt solutions
Authors: Sharp Dan S. , Ifft James B. 
Published: December 2004

AbstractEarlier determinations of density gradient proportionality constants β0, density distributions ρ(r), and the effect of pressure on density gradients in the analytical ultracentrifuge have been of limited precision and usefulness in the study of proteins and polypeptides. Reasons for these difficulties are that numerous intermediate relationships were required in the calculations, and the density ranges studied were generally above 1.2 g/ml. Relations are derived in the present paper to directly compute β0(ρ) values and β0′(ρ) values from the original data without any intermediate expansions or approximations. Data are presented for CsCl, CsBr, and Cs2SO4 and compared with literature values. Density distributions are computed for all three salts under a wide variety of experimental conditions of density, column length, and angular velocity. These values of ρ(r) and re are obtained by a numerical iterative technique. Values obtained by this new method are compared with values obtained using closed‐form expressions. The effects of pressure on the composition density gradient for the three salts given above are calculated and found to be significant for Cs2SO4 solutions.
Vibrational analysis of peptides, polypeptides, and proteins. VI. Assignment of β‐turn modes in insulin and other proteins
Authors: Bandekar Jagdeesh , Krimm S. 
Published: December 2004

AbstractThe normal modes have been calculated for structures having the dihedral angles of the four β‐turns of insulin. Frequencies are predicted in the amide I region near 1652 and 1680 cm−1. The former overlaps the α‐helix band at 1658 cm−1 in the Raman spectrum, while the latter accounts for the hitherto unassignable band at 1681 cm−1. Calculated amide III frequencies extend above 1300 cm−1, providing a compelling assignment of the 1303‐cm−1 band in insulin and similar bands in other globular proteins.
Chemical reactivity of protonated aziridine with nucleophilic centers of DNA bases
Authors: Kikuchi O. , Hopfinger A. J. , Klopman G. 
Published: December 2004

AbstractA series of molecular orbital calculations, using MINDO/3 and CNDO/2L methods, have been used to characterize the chemical reaction of protonated aziridine with DNA nucleophilic base sites. The N‐7 atom of guanine is found to be the preferred alkylation site only when the O‐6 atom of guanine is involved in base‐pair hydrogen bonding. Otherwise O‐6 is the predicted major site of alkylation. This indirectly suggests that protonated aziridine alkylation processes involve base‐paired DNA structures, since N‐7 guanine is the observed major site of alkylation. Alkylation of N‐3 adenine is predicted to be more favorable than chemical attack of the N‐7 adenine position. Both of these sites, however, are predicted to be less reactive than N‐7 of guanine. These chemical reactivity studies resolve alkylation specifically not achieved in the DNA–alkylator physical association calculations reported in the preceding paper.
Conformational analysis of somatostatin and selected analogs in oriented polyoxyethylene by infrared dichroism
Authors: Gilon C. , Simmons D. , Goodman M. , Rivier J. 
Published: December 2004

AbstractInfrared dichroic studies and deuterium exchange measurements of somatostatin and some of its analogs incorporated in uniaxially oriented polyoxyethylene are described. Band positions and dichroic ratios in the N‐H stretching and amide I and II regions are similar to those of flexible and nonordered peptides like valinomycin and poly[Glu(ONa)]. This information, together with fast deuterium exchange rates, suggests that somatostatin exists in a flexible nonordered conformation in polyoxyethylene. One analog, di‐S3,14‐acetamidomethyl dihydrosomatostatin, was found to exist in both nonordered and β‐like conformations.
Study of salt effects on adenosine–polyuridylic acid interaction
Authors: Gukovskaya A. S. , Gukovsky I. Ya. , Chikh V. P. , Sukhorukov B. I. 
Published: December 2004

AbstractComplex formation between poly(U) and adenosine in solutions of salts that stabilize (Na2SO4), destabilize (NaClO4), or have little effect on the water structure (NaCl), as well as the poly(U)·poly(A) interaction in NaClO4, was studied by equilibrium dialysis and uv spectroscopy. At 3°C and neutral pH, Ado·2 poly(U) is formed in 1M NaCl and 0.33M Na2SO4. In NaClO4 solutions under the same conditions, an Ado·poly(U) was found over the whole range of salt concentration investigated (10 mM−1M), which has not been previously observed under any conditions. The Ado‐poly(U) was also found in a NaCl/NaClO4 mixture, the transition from the triple‐ to the double‐helical complex occurring within a narrow range of concentration of added NaClO4. In the presence of 1M NaCl this transition is observed on adding as little as 10 mM NaClO4, i.e., at a [ClO]/[Cl−] ratio of about 1:100. However, when NaClO4 is added to a 1M solution of the stabilizing salt Na2SO4, no transition occurs even at a [ClO]/[SO] ratio of 1:4. Investigation of melting curves and uv spectra has shown that in an equimolar mixture of the polynucleotides, only a double‐helical poly(U)·poly(A) exists in 1M NaClO4 at low temperatures; this also holds for 1M NaCl. This changes to a triple‐helical 2 poly(U)·poly(A) and then dissociates as the temperature increases. At low temperatures and the poly(U)/poly(A) concentration ratio of 2:1, a mixture of 2 poly(U)·poly(A) and poly(U)·poly(A) was observed in 1M NaClO4, in contrast to the case of 1M NaCl. Thus, sodium perchlorate, a strong destabilizer of water structure, promotes formation of double‐helical complexes both in the polynucleotide–monomer and the polynucleotide–polynucleotide systems.Beginning with a sufficiently high ionic strength (μ ≃ 0.9), a further increase in the salt molarity results in an increase of the poly(U)·adenosine melting temperature in both stabilizing and neutral salts and a decrease in the destabilizing salt. In Na2SO4 concentrations higher than 1.2M Ado·2 poly(U) precipitates at room temperature. Analysis of the binding isotherms and melting profiles of the complexes between poly(U) and adenosine according to Hill's model shows that the cooperativity of binding, due to adenosine stacking on poly(U), increases in the order NaClO4 < NaCl < Na2SO4. The free energy of adenosine stacking on the template is similar to that of hydrogen bonding between adenosine and poly(U) and ranges from −1 to −2 kcal/mol. The values of ΔHt [the effective enthalpy of adenosine binding to poly(U) next to an occupied site, obtained from the relationship between complex melting temperature and free monomer concentration at the midpoint of the transition] are −14.2, −18.3, and −16.8 kcal/mol for 1M solutions of NaClO4, NaCl, and Na2SO4, respectively. The results indicate that the effects of anions of the salts studied are related to water structure alterations rather than to their direct interaction with the complexes between poly(U) and adenosine.
Application of band centrifugation to the study of the assembly of alfalfa mosaic virus
Authors: Driedonks René A. , Joe Michael K. K. Tjok , Mellema Jan E. 
Published: December 2004

AbstractA band‐centrifugation method for the analysis of an assembly reaction of a simple virus from its RNA and protein is described. The experiment was carried out by sedimenting a band of viral RNA through a solution of depolymerized coat protein. The resulting radial distribution of the reaction products, followed as a function of time, was analyzed by a computer simulation of the series of reaction. This method is based on a numerical solution of the continuity equation for the sedimentation–diffusion process [Claverie, J.‐M., Dreux, H. & Cohen, R. (1975) Biopolymers 14, 1685–1700; Cohen, R. & Claverie, J.‐M. (1975) Biopolymers 14, 1701–1716]. A numerical method for the simulation of the chemical reaction is derived. From the simulated reaction series, equilibrium constants emerge for the successive addition of protein subunits to the growing nucleoprotein particle.The method is applied to the assembly of alfalfa mosaic virus. If the reaction between RNA and protein is carried out in 0.32M CsCl, pH 7.0, two stages during particle growth are resolved, each characterized by an equilibrium constant K. The determined values for K range from 5 × 105 to 3 × 106 l. mol−1. The existence of these two stages may have a structural implication in the assembly, as they likely represent an elongation and a termination stage. If the reaction is carried out under more favorable conditions (0.25M CsCl, pH 7.0), a kinetic constant of at least 105 l. mol−1 sec−1 is derived for each reaction step. Under these conditions the assembly appears to be completed within 1 min, which is too fast to detect distinct stages by band sedimentation.
Monte carlo computation of the supercoiling energy, the sedimentation constant, and the radius of gyration of unknotted and knotted circular DNA
Authors: Le Bret Marc 
Published: December 2004

AbstractClosed random Gaussian polygonal chains of N (6 < N < 150) bonds of equal length b and thickness d have been generated on a computer. The knot type, the writhing number w, the radius of gyration, and the average of the inverse of the distance between two apices have been determined for each chain. For all the studied knot types—0, 31, 41, 51, and 52—the probability density of finding a given w is Gaussian. The Gaussian is centered about 0 for the amphichiral knots. Therefore, for long circular DNAs, the contribution to the supercoiling energy, which depends on w only, may be considered as purely entropic and may be expressed as ARTw2/N, in agreement with previous semiempirical considerations. The parameter A increases with chain thickness, it decreases as N gets larger but rapidly reaches a plateau. Comparison with experimental data from the literature would suggest that the ratio of the writhing to the constraint increases with ionic strength. The ratio of sedimentation constant of the supercoiled DNA to the sedimentation constant of the nicked DNA varies as N1/4 (w/N)2, and therefore depends on the writhing density and on the length of the DNA.
Measurement of preferential solvation of some glucans in mixed solvent systems by gel‐permeation chromatography
Authors: Straub Peggy R. , Brant David A. 
Published: December 2004

AbstractPreferential solvation of the glucans amylose, pullulan, and dextran in binary dimethyl‐sulfoxide/water (DMSO/H2O) solvent mixtures has been measured using gel‐permeation chromatography. The preferential solvation behavior of the three glucans in DMSO/H2O solvent mixtures is indistinguishable in the experiments reported. In solvent mixtures with mol ratio DMSO/H2O less than 1:2, all three glucans are solvated preferentially by H2O. The maximum extent of preferential solvation by H2O is about 2.5 mol H2O/mol of glucose residues. When the DMSO/H2O mol ratio exceeds 1:2, DMSO solvates the glucans preferentially to a maximum extent of about 1 mol DMSO/mol of glucose residues. An interpretation of the change in preferential solvation with mixed solvent composition is suggested in terms of the known characteristics of the binary solvent system, and the relationship of preferential solvation, reported here, to the absolute solvation of the glucan chains is discussed.
Electrical conductivity of single crystals of lysozyme
Authors: Ataka Mitsuo , Tanaka Shoji 
Published: December 2004

AbstractThe dc electrical conductivity of large single crystals of hen egg‐white lysozyme has been measured. The samples were grown from aqueous solution and dried in air with silica gel. The temperature dependence of the conductivity obeyed the relation σ = σ0 exp(− ΔE/kT), with ΔE = 1.2 eV. The ΔE value agreed with most of the previous results for various proteins in the form of lyophilized powder. On the other hand, log σ0, being between 7 and 11, was much larger than the previously reported values and differed among the samples. An irreversible decrease in σ0, without affecting ΔE, was observed on heating the samples above 85°C. It was shown that the set of results can be explained if the charge carriers responsible for the observed conduction are regarded as protons, originating from residual water molecules. Photoresponse of the samples to uv radiation below 305–315 nm was also observed. Reproducible and reliable results were obtained relatively easily in the present experiments, which is thought to be the main advantage of using single‐crystalline samples.
Transport properties and hydrodynamic centers of rigid macromolecules with arbitrary shapes
Authors: Bernal José M. García , De La Torre José García 
Published: December 2004

AbstractA general formalism, which includes translation–rotation coupling, is proposed for calculating translational and rotational transport properties, as well as intrinsic viscosities, of rigid macromolecules with an arbitrary shape. This formalism is based on Brenner's theory of translational–rotational dynamics and on methods for the calculation of hydrodynamic properties that have been already presented, and can be regarded as a generalization of the one proposed by Nakajima and Wada. The calculated transport properties depend on the origin as predicted by Brenner's theory, but in a disagreement with him, the center of resistance and the center of diffusion do not coincide. As one can define several hydrodynamic centers, which in practice turn out to be located at different points, the influence of the choice of the center on the calculated transport properties is discussed. An analysis of the translation–rotation coupling effects in translational diffusion reveals that they arise exclusively from hydrodynamic interactions and are rather small in some cases of interest. Finally, we present a study of the rotational diffusion of rigid bent rods with a fixed length‐to‐diameter ratio. The diffusion coefficients obtained can be useful to estimate changes with respect to a straight rod.
Effects of glycosaminoglycans and proteoglycan on the in vitro assembly and thermal stability of collagen fibrils
Authors: Snowden John McK. , Swann David A. 
Published: December 2004

AbstractThe effects of three glycosaminoglycans (chondroitin 6‐sulfate, dermatan sulfate, and hyaluronate) and a proteoglycan on the kinetics of fibril formation and on the thermal stability of the in vitro assembled collagen fibrils, under physiological conditions of ionic strength and pH, have been examined. The glycosaminoglycans were found to influence the kinetics of collagen precipitation but not the thermal stability of the in vitro assembled fibrils. The proteoglycan was found to influence the kinetics of collagen precipitation and to reduce the thermal stability of the in vitro assembled fibrils. Comparison of the interaction occurring between chondroitin 6‐sulfate and collagen under acidic conditions (0.05M acetic acid) and that occurring under physiological conditions showed that markedly different interaction products were formed under the different conditions.
NMR evidence for a type I β‐turn in (Pro2)‐tetrapeptides and interdependence of cis:Trans isomerism, ring flexibility, and backbone conformation
Authors: Toma Flavio , Lam‐Thanh Hung , Piriou François , Heindl Marie‐Christine , Lintner Karl , Fermandjian Serge 
Published: December 2004

AbstractTetrapeptides with proline in position 2, asparagine or leucine in position 3, and glycine in positions 1 and 4, with end groups free or blocked on the N‐terminal side, were studied in their various ionic states in 2H2O and in Me2SO‐d6 by 1H‐ and 13C‐nmr. In order to clarify or refine some details, successive substitutions of the residues in these peptides with amino acids enriched to 85% in 13C, or to 85% 13C plus 97% 2H were carried out. The 1H and 13C chemical shifts as well as the 1H‐1H, 13C‐13C, and 13C‐1H coupling constants and the signal intensities show strong similarity of behavior between the tetrapeptides of asparagine and leucine. The main conformational characteristics are (1) the almost total stabilization of the trans conformer in the type I β‐turn structure when the peptide is in the zwitterion state dissolved in Me2SO. This is deduced from the 3J and the 3J coupling constants, which both furnish a dihedral angle of ϕ3 = −90°, and from the positive value of the temperature coefficient of the glycine‐4 amide protons, which suggests a type 4 → 1 hydrogen bond; (2) the evolution of cis and trans isomer fractions which change with the ionic state of the peptides in Me2SO, whereas they remain constant in aqueous solution; and (3) the conformation of the pyrrolidine ring as it follows the variations in cis:trans isomer populations together with the side‐chain rotamer fractions of the residue in position 3. In the β‐turn conformation the isomer cis is less abundant and the pyrrolidine ring is more flexible; this explains the perfect accommodation of the proline residue in position 2 of a bend. The interdependence of these phenomena where interactive forces play a predominant role underlines the importance of cooperative effects in the molecule. The results also suggest that the cis isomer of proline can adapt itself just as well as the trans isomer to position 2 of a type I β‐turn.
Potentiometric titration curves of oxidized and reduced horse heart cytochrome c
Authors: Marini M. A. , Marti G. E. , Berger R. L. , Martin C. J. 
Published: December 2004

AbstractPotentiometric titration curves of oxidized and reduced horse heart cytochrome c in 0.15M KCl at 20°C have been obtained by timed titration (0.125–0.500 μmol/sec) from the isoionic points (pH 10.2–10.4) to pH 3 and back to the isoionic point. Computer‐assisted (PROPHET) data acquisition and blank corrections give curves with good precision with a maximum standard deviation of 0.3 groups for an average error of 1%. The potentiometric titration curve of reduced cytochrome c is reversible within the precision of the method and for the pH range studied. The potentiometric curves for oxidized cytochrome c titrated upscale (pH 3–10) and downscale (pH 10–3) are not reversible. However, they show the same ionization behavior after the initial downscale titration. This is probably the result of a conformational change. Comparison of the data herein reported with the titration curves of oxidized cytochrome c already published by others indicates good agreement on the basis of a normalization of the concentration of protein or on the basis of 25 titrable groups between the acid end point and the isoionic pH.Titration of the 2 μmol imidazole in the upscale or downscale direction gives the correct analytical concentration and pK′ after correction for the solvent titration. Titration of reduced cytochrome c in the presence and absence of an additional equivalent of imidazole gave a difference titration curve, which indicates that a group on the protein shifts from pK′ 5.8 to pK′ 5.3 in the presence of imidazole. The pK′ of imidazole, in the presence of the protein, remains at a nearly normal value of 7.34.
Effects of pH and ionic strength on the structure of collagen fibrils
Authors: Ripamonti A. , Roveri N. , Braga D. , Hulmes D. J. S. , Miller A. , Timmins P. A. 
Published: December 2004

AbstractThe roles of pH and ionic strength on the structure and stability of collagen fibrils have been investigated by means of x‐ray and neutron diffraction techniques. High‐angle x‐ray diffraction shows that a salt concentration of 0.5M KCl is sufficient to reduce the osmotic swelling and related disordering in the pH range 1–3. The relative intensities of the low‐angle meridional x‐ray and neutron diffraction Bragg reflections vary with pH. Difference Fourier syntheses between pH 7 and 1.6 data indicate, for both x‐ray and neutron diffraction, a reduced scattering contribution from the telopeptides at low pH. Lyotropic relaxation is a crucial step in the appearance at low pH of a doubling of the 668‐Å axial periodicity (D) of collagen fibrils. These results suggest that electrostatic interactions are essential for the structural stability of the telopeptide regions and of the 1D and 3D intermolecular staggers between collagen molecules.