bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sol–sol structural transition of aqueous agarose systems
Authors: Biagio P. L. San , Madonia F. , Newman J. , Palma M. U. 
Published: December 2004

AbstractA structural transition is reported to occur in aqueous sols of agarose, an electrically uncharged biostructural polysaccharide. The transition has no measurable effect on size dispersity on the shape of the solute polysaccharide as observed by precision photon correlation spectroscopy. It originates a low‐angle pattern of scattered light similar to that which monitors phase separations in polymer blends. Thus, it must be due to some extent to spatially modulated polymer clustering, typical of spinodal decomposition. In the interval of temperatures studied, it precedes very distinctly in time the thermoreversible sol–gel transition, which is known to be promoted at higher concentrations. It also anticipates to an appreciable extent the spatial density modulation observed in the gel. Although reported here for the first time, a spinodal decomposition of the sol that precedes and possibly triggers the processes leading to gelation does not come unexpectedly in terms of site‐bond correlated‐percolation theory. In general, this occurrence raises the question as to whether the spontaneous onset of regions of higher and lower polymer concentration (spinodal separation) may be regarded as a novel path for biomolecular interactions and the self‐assembly of order in biomolecular systems.
Evidence for a folded structure of met‐enkephalin in membrane mimetic systems: 1H‐nmr studies in sodiumdodecylsulfate, lyso‐phosphatidylcholine, and mixed lyso‐phosphatidylcholine/sulfatide micelles
Authors: Zetta Lucia , De Marco Antonio , Zannoni Giulio , Cestaro Benvenuto 
Published: December 2004

Abstract1H‐nmr spectra of Met‐enkephalin dissolved in aqueous solution of sodiumdodecylsulfate (SDS) micelles are reported as a function of pH and temperature. The temperature behavior of the amide protons is compared with that observed for the same peptide dissolved in aqueous solution of lyso‐phosphatidylcholine (LPC) and lyso‐phosphatidylcholine‐sulfatide (LPC‐SH) micelles. The temperature coefficients are affected by the micelle polarity, which suggests that the peptide backbone is not remote from the micelle surface. pH titration performed in the presence of SDS micelles gives a number of intrinsic and extrinsic pKa values, indicative of a folded structure of the opioid molecule. This conformation is characterized by the existence of an intramolecular hydrogen bond involving the Met‐5 amide proton and an interaction of the N‐terminal residue with the aliphatic side chains of both Phe‐4 and Met‐5.
Lateral packing of protofibrils in fibrin fibers and fibrinogen polymers
Authors: Voter William A. , Lucaveche Carmen , Blaurock Allen E. , Erickson Harold P. 
Published: December 2004

AbstractThe distinctive transverse banding pattern of fibrin fibers clearly indicates ordering of molecules in the longitudinal direction. In this study we examined the fibers of fibrin clots, as well as two types of fibrinogen polymers, by thin‐section electron microscopy. The fibrinogen polymers have a transverse banding pattern identical to that of fibrin fibers—clearly indicating a regular longitudinal repeat—but they are larger in diameter, and show little or no branching. We therefore expected their overall ordering to be better than that of fibrin fibers. Several different fixation protocols were used. We readily observed the typical transverse banding seen previously by negative stain and metal replication techniques. However, only very rarely was any regular lateral lattice seen in any of the samples. X‐ray diffraction was used to examine unfixed specimens of the two fibrinogen polymers and, once again, although a longitudinal repeat was evident, only rarely was evidence for lateral crystallinity seen. The electron‐microscope and x‐ray results showed that the needles and pellet fibers of fibrinogen have essentially the same internal architecture as thick fibrin fibers, and that all three types of polymer, although clearly transversely banded, have almost no crystallinity in their lateral protofibril packing.
The influence of calcium ions on fibrin polymerization
Authors: Häberli A. , Straub P. W. , Dietler G. , Känzig W. 
Published: December 2004

AbstractThe influence of calcium ions on the polymerization induced in fibrinogen solutions by thrombin and by Reptilase has been investigated by meansof static and dynamic light scattering in combination with measurements of the release of the fibrinopeptide A. The calcium concentration was varied in the range between 0.3 and 103 calcium ions per fibrinogen molecule. The enzyme concentration was chosen sufficiently low so that it was possible to make quantitative observations as a function of time, in particular, beforethe onset of gelation. Likewise, the influence of calcium ions on the enzymatically induced polymerization of fragment X was studied. The results indicate that there are at least three mechanisms by which calcium can influence the evolution of the polymer system on the path to gelation and clotting. Which mechanism dominates depends upon the calcium concentration.
Crystal structure and molecular conformation of the tripeptide, N‐Boc‐L‐Phe‐Dehydro‐Phe‐L‐Val‐OCH3
Authors: Singh T. P. , Haridas M. , Chauhan V. S. , Kumar A. , Viterbo D. 
Published: December 2004

AbstractThe tripeptide, N‐Boc‐L‐Phe‐dehydro‐Phe‐L‐Val‐methyl ester (C29H37N3O6) was synthesized as a model peptide to produce a specific β‐turn with the help of dehydro‐Phe. This peptide crystallizes in the triclinic space group Pl with a = 6.085(2) Å, b = 9.515(4) Å, c = 13.243(5) Å, α = 105.16(3)°, β = 92.69(3)°, γ = 104.9(3)°, and Z = 1. The structure was solved by direct methods using MULTAN 80. The structure was refined by the block‐diagonal least‐squares method to an R value of 0.075 for 2438 observed reflections. The bond lengths and angles, in general, are in good agreement with the standard values. The peptide backbone adopts the β‐conformation as a result of deprotonation at the Cα and Cβ atoms in the dehydro‐Phe residue. The backbone conformations around the Cα atoms are cis, and the corresponding moieties are nonplanar. The backbone segments between the Cα atoms have extended trans conformations with highly planar configurations. The chain conformation angles—ϕ1, ψ1, ω1, ϕ2, ψ2, ω2, ϕ3, and ψ—are −45.4(11)°, −45.6(6)°, − 179.3(4)°, −46.5(5)°, −38.0(6)°, 165.3(9)°, 51.7(5)°, and 43.0(6)°, respectively. The phenyl rings of Phe and dehydro‐Phe are essentially planar and their planes are inclined with respect to each other at 69.7(5)°. The CβCγ bonds in Phe and dehydro‐Phe are trans with respect to the NCα bonds, with a X1 torsion angle (about CαCβ) of −176.3(1)° and −179.4(5)°, respectively. The C′Cα bonds are cis and trans with respect to the CβCγ bonds, with torsion angles of −56.8(7)° and −170.0(16)° in Phe and dehydro‐Phe, respectively. The β‐turn conformation is stabilized by an intramolecular hydrogen bond, N3H3 …︁ O2, of a distance of 3.116(6) Å. The molecules are held in the crystal structure by a network of hydrogen bonds and the van der Waals forces.
Cystine peptides: The intramolecular antiparallel β‐sheet conformation of a 20‐membered cyclic peptide disulfide
Authors: Kishore R. , Raghothama S. , Balaram P. 
Published: December 2004

AbstractA 20‐membered cyclic peptide disulfide magnified image has been synthesized as a conformational model for disulfide loops of limited ring size. 1H‐nmr studies at 270 MHz establish the presence of three intramolecular hydrogen bonds involving the Leu, Val, and methylamide NH groups in CDCl3. Evidence for peptide aggregation in CDCl3 is also presented. A structural transition involving loosening of the hydrogen bond formed by the Val NH group is observed upon the measured addition of (CD3)2SO to CDCl3. Hydrogen‐bonding studies, together with unusually low field positions of the Cys(1) and Cys(6) CαH resonances and high J values provide support for an intramolecular antiparallel β‐sheet conformation, facilitated by a chain reversal at the Aib‐Ala segment. Extensive nuclear Overhauser effect studies provide compelling evidence for the proposed conformation and also establish a type I′ β‐turn at the Aib‐Ala residues, the site of the chain reversal.
Raman spectroscopic study on low‐frequency collective modes in self‐associates of guanosine monophosphates
Authors: Urabe Hisako , Sugawara Yoko , Tsukakoshi Motowo , Ikegami Akira , Iwasaki Hitoshi , Kasuya Takahiro 
Published: December 2004

AbstractLow‐frequency Raman spectra of the self‐associates of guanosine monophosphates (GMPs) Na2 · 5′GMP, K2 · 5′GMP, Na2 · 3′GMP, and K2 · 3′GMP, and polyribonucleic acid K · poly(rG), were obtained. In acidic gels and dried fibers, GMP molecules are known to form helical stacks of hydrogen‐bonded tetramers. Some low‐frequency collective modes specific to the helically stacked structures were observed. We examined the dependence of these modes on counterions and water content. The lowest frequency mode at ca. 20 cm−1 is sensitive to the water content of the sample and is clearly visible in solid‐state samples, so it works as a marker band of the environmental condition of the helices. The intensity and the peak frequency of this mode in solid‐state samples depend on the helical structure and counterions. The broad peaks in the vicinity of 100 cm−1 are influenced by cations and are independent of water content.
Molecular mechanics studies of parallel and antiparallel phosphate‐methylated DNA
Authors: Van Genderen Marcel H. P. , Koole Leo H. , Aagaard Olav M. , Van Lare Coert E. J. , Buck Henk M. 
Published: December 2004

AbstractMethylation of phosphate groups in oligo‐dT strands leads to a parallel duplex with T · T base pairs. Molecular mechanics calculations on parallel d(TTTTTT)2 show it to be a symmetric right‐handed helix with B‐DNA conformational characteristics. Phosphate methylation stabilizes the duplex by ca. 41 kcal/mol, due to removal of the interstrand phosphate electrostatic repulsions. The chirality introduced with phosphate methylation is important for the molecular geometry, since RP methylation predominantly influences the conformation around the ζ bond (PO3′), while SP methylation mostly changes the α conformation (PO5′). This is also true in antiparallel helices with methylated phosphates, as is shown by molecular mechanics calculations on d(GCGCGC)2. These results may be of relevance to protein–DNA interactions, where phosphate charges are also shielded. As the pro‐SP oxygen is most available in a right‐handed helix, we suggest changes around the α bond to occur upon protein complexation, leading to a widening of the major groove in the d(GCGCGC)2 duplex (from 12 to 13 Å) and reduced minor groove (from 6 to 5 Å).
The melting behavior of a DNA junction structure: A calorimetric and spectroscopic study
Authors: Marky Luis A. , Kallenbach Neville R. , McDonough Kathleen A. , Seeman Nadrian C. , Breslauer Kenneth J. 
Published: December 2004

AbstractWe present an investigation of the helix–coil transition in a stable branched oligomer of DNA, known as an immobile DNA junction. This junction is composed of four 16‐mer strands, which yield four double‐helical arms, each containing 8 nucleotide pairs. Properties of the individual arms of this complex are modeled by four octameric duplexes. We have performed experiments using calorimetry, uv absorbance, and CD spectroscopy to characterize the melting transitions of the junction and each arm. By comparing our spectroscopic and calorimetric results on the junction and its component arms, we are able to conclude the following: (1) The calorimetric transition enthalpy for the overall junction complex is equal to the sum of the calorimetric transition enthalpies of the four constituent duplex arms. (2) The optical and the calorimetric measurements yield qualitatively similar, but not identical thermodynamic data. (3) The melting temperature of the junction is less dependent on concentration than the melting temperatures of the individual arms. We attribute this observation to the tetrameric nature of the junction. (4) The ratio of the calorimetric transition enthalpy of the junction and its corresponding van't Hoff value is close to unity. (5) The CD spectrum of the junction is equal quantitatively to the sum of the B‐like CD spectra of the four constituent duplex arms.
Application of the augmented theory of α‐helix‐to‐random‐coil transitions of two‐chain, coiled coils to extant data on synthetic, tropomyosin‐analog peptides
Authors: Holtzer Alfred , Skolnick Jeffrey 
Published: December 2004

AbstractThe statistical mechanical theory for the helix‐to‐random‐coil transition in two‐chain coiled coils is applied to extant data for two synthetic coiled‐coil polypeptides. These peptides have the primary structure K(LEALEGK)n, in which n = 4, 5. This repeating heptet sequence mimics the pattern of hydrophobic, acidic, and basic residues characteristic of the 284‐residue tropomyosin molecule, the prototypical coiled‐coil protein. Theoretical calculations for single chains show that such model peptides cannot be directly compared to proteins like tropomyosin because of differences in chain length (29 and 36 residues vs 284) and in intrachain interactions, the latter caused by the differences in amino acid composition and seqeunce between protein and model. Application of the theory to extant data on the two synthetic peptides provides a semiquantitative fit and results in an assessment of the interhelix interaction in the model peptides. The value obtained, ∼ 2000 cal · (mol of turn pairs)–1, is four to five times larger than has been obtained for tropomyosin. This probably is a result of greater regularity in the structure of the synthetics and of the exclusive presence of leucine in the hydrophobic interface. The theory employed here insists that this powerful interhelix interaction in the synthetic is the principal reason that such short chains can be so highly helical at moderate and low temperatures. Theory predicts, indeed, that a tropomyosin‐length chain with a sequence homologous to these synthetics would be completely thermally stable in the entire temperature range accessible in aqueous solutions. Theory also predicts a much more pronounced effect of concentration on the 29‐ and 36‐residue synthetic polymers than is predicted or observed in the case of tropomyosin, and it also predicts a pronounced stabilizing effect of pH‐reduction on the thermal curves. On the last two points, sufficient data are not yet available with which to test the theory.
The structure of agarose gels, and the accommodation within them of irregularly shaped particles
Authors: West Roger 
Published: December 2004

AbstractThis paper shows how the number of cross‐linkage points (nodes) in a random reticulum, such as an ideal polysaccharide gel, may be calculated in accordance with mathematical principles. The influence of nodal configurations upon the statistical geometry of the reticulum is discussed, and it is shown from experimental evidence that the nodal configurations in agarose gel are nonrandom. A method is given for calculating the accommodation probability of an irregularly shaped particle in a reticulum, which is relevant to the theory of gel chromatography and to the distribution of cells in tissues permeating a network of capillaries or veins.
Determination of thermodynamic functions from scanning calorimetry data. II. For the system that includes self‐dissociation / association process
Authors: Kidokoro Shun‐Ichi , Uedaira Hatsuho , Wada Akiyoshi 
Published: December 2004

AbstractThe basic relations between the molar fractions and the scanning calorimetry data for the system that includes self‐dissociation/association process such as

are presented, where mi is the stoichiometric coefficient of the ith state Ai. The relations are described for each state j as

where fj(T) is the molar fraction function of state j and ΔHj(T) is the difference enthalpy function of the system referred to the state j, which can be obtained by scanning calorimetry; R is the gas constant; and T is the absolute temperature. By these relations, scanning calorimetry data can be deconvoluted in order to determine the thermodynamic functions by means of single and double deconvolution. The concentration dependence of the data is analyzed by a method presented in this paper. The nonlinear least squares fitting method for the determination of the functions is discussed. For an example of the application of this method to the actual scanning calorimetry data, thermodynamic data of multistate thermal transition of Vibrio parahaemolyticus hemolysin are analyzed.
Distance distributions in native and random‐coil troponin I from frequency‐domain measurements of fluorescence energy transfer
Authors: Lakowicz Joseph R. , Gryczynski Ignacy , Cheung Herbert C. , Wang Chien‐Kao , Johnson Michael L. 
Published: December 2004

AbstractWe used time‐dependent fluorescence energy transfer to determine the distribution of donor‐to‐acceptor distances in native and denatured troponin I(TnI). The single tryptophan residue (Trp 158) of TnI served as the donor (D), and the acceptor (A) was a labeled cysteine residue (Cys 133). The time‐dependent intensity decays of the donor were measured by the frequency‐domain method from 10 to 320 MHz. The frequency response of the donor emission, in the absence and presence of acceptor, was used to recover the distribution of D to A distances, using an algorithm that accounts for the intrinsic multiexponential decay of the donor. In the native state the D–A distribution is characterized by an average distance of 23 Å and a half‐width of 12 Å. Denaturation results in a modest increase in the average distance to 27 Å, and a dramatic increase in half‐width to 47 Å. We believe the ability to recover distance distributions will have numerous applications in the characterization of biological macromolecules.
Study of the bisintercalation of the antitumor drug ditercalinium by 31P‐nmr
Authors: Delepierre Muriel , Igolen Jean , Roques B. P. 
Published: December 2004

AbstractBisintercalation of ditercalinium, a potent antitumoral 7H‐pyriodo[4,3‐c]carbazole rigid dimer, into the self‐complementary tetranucleotides d(CpGpCpG)2, d(m5CpGpm5CpG) and the self‐complementary hexanucleotide d(CpGpApTpCpG)2 was investigated by 162‐MHz 31P‐nmr. The slow exchange, on the nmr time scale, observed between the free and complexed nucleotides allows identification of the phosphorus signals in the complexes through two‐dimensional chemical exchange spectroscopy. Differences in 31P chemical shifts upon intercalation are discussed in relation to the complex geometry and nature of the drug.
Conformational studies of N‐acetyl‐N′‐methylamide derivatives of α‐aminobutyric acid, norvaline, and valine. I. Preferred conformations in solution as studied by 1H‐nmr spectroscopy
Authors: Yamazaki Toshimasa , Abe Akihiro 
Published: December 2004

AbstractThe 1H‐nmr studies were extensively carried out to elucidate preferred conformations of dipeptides CH3C*O—X—NHCH3, with X = Abu, nVal, and Val in various solvents. The vicinal 1H—1H coupling constants for the NH—CαH moiety and those around the Cα—Cβ bond in the articulated side chain provided the information regarding the average conformation of these molecules. The results indicate that transformation of skeletal conformations takes place in solution among conformers having similar dihedral angles, θ, in the Karplus expression.
Frictional models for stochastic simulations of proteins
Authors: Venable Richard M. , Pastor Richard W. 
Published: December 2004

AbstractAs a first step toward a systematic parametrization of friction constants of atoms in proteins, a model in which frictional resistance is placed explicitly on each atom accessible to solvent is used to calculate overall translational and rotational diffusion constants. It is found that these quantities are relatively insensitive to the precise value of the atomic friction constant, as long as the effective hydrodynamic radius of the surface atoms is approximately 1 Å. However, if only protein atoms are included in the calculation, no reasonable range atomic of radii can reproduce the experimental translational diffusion constant to better than 20% for lysozyme and 5% for ribonuclease. When a hydration shell of approximately 70% coverage for lysozyme and 20% for ribonuclease is included, there is quantitative agreement with experimental results. The sensitivity of peptide diffusion to levels of hydration is also investigated; it is found that for glycine, two bound waters are required to provide agreement with experiment. These findings imply that the effects of solvent damping will be underestimated in stochastic simulations of proteins and peptides unless bound waters are taken into account.
13C‐nmr spectroscopic investigation of two yeast cell wall β‐D‐glucans
Authors: Kogan Grigorij , Alföldi Juraj , Masler Ladislav 
Published: December 2004

AbstractBy means of alkaline extraction of the cell walsl of the yeasts Saccharomyces cerevisiae and Canadida albicans, water‐insoluble glucans were obtained. Methylation analysis and 13C‐nmr investigation in dimethyl sulfoxide solution revealed the similar chemical structure of these glucans, being composed of β(1 → 3) glycosidically linked D‐glucopyranosyl units with a small amount of β(1 → 6) linkages. More detailed study in dilute alkaline solutions and in the gel state at neutral pH, however, showed that an ordered helical conformation of the glucan chain is less stable in the case of the S. cerevisiae glucan in comparison with that of C. albicans. Measurements of the shift of the absorption maximum of the glucan complexes with Congo Red also demonstrated such difference. The S. cerevisiae glucan was also inable to form a gel at neutral pH. The difference in stability of helical conformation of the glucans is explained on the basis of the methylation analysis, so that the S. cerevisiae glucan possesses longer side chains, which hinder its adoption of a stable helical conformation.
Effects of pH and temperature on cardioactive polypeptides from sea anemones: A 1H‐nmr study
Authors: Gooley Paul R. , Blunt John W. , Beress Laszlo , Norton Raymond S. 
Published: December 2004

AbstractThe effects of pH and temperature on the 300‐MHz 1H‐nmr spectra of three cardioactive polypeptides from sea anemones, anthopleurin‐A from Anthopleura xanthogrammica (AP‐A) and Anemonia sulcata toxins I and II (ATX I and II), are described. AP‐A and ATX II exhibit major spectral heterogeneity. Evidence from the pH and temperature studies and from high performance liquid chromatography indicates that this heterogeneity is conformational rather than chemical in origin. By contrast, purified isotoxins of ATX I show no evidence of conformational heterogeneity. The pKa values of most of the ionizable groups in these polypeptides are not strongly perturbed by interactions in the tertiary structure, with the exception of one of the Asp carboxylates, which has a pKa of ≲ 2 in AP‐A and ATX II and 3.0 in ATX I. Protonation of this carboxylate, suggested to be Asp‐9, leads to a conformational change in all three molecules. All three polypeptides are thermally stable, showing some conformational changes but not major unfolding at elevated temperatures.