bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circular dichroism of corticotropin, fragment 1–24, and model compounds. An assessment of the contributions of the peptide chromophore and aromatic residues
Authors: Holladay Leslie A. , Puett David 
Published: December 2004

AbstractThe far‐ultraviolet circular dichroic spectrum of the 39‐residue peptide hormone porcine corticotropin and the biologically active fragment corticotropin 1–24 is negative from 250 nm to 195 nm in water, but in 6M guanidinium chloride a positive band appears at about 225 nm. The temperature and guanidinium chloride dependence of this spectral transition indicates the absence of any stable ordered secondary structure in corticotropin and the spectrum is seen to be in only partial agreement with results using the model peptide chromophore, Ala‐Ala‐Ala. Using oligopeptides containing aromatic amino acid residues sandwiched between glycyl residues, it is shown that the shape and intensity of the corticotropin 225 nm positive band which appears in 6M guanidinium chloride is in agreement with the far‐ultraviolet transitions of the aromatic chromophores in the hormone. Curve resolution of the near‐ultraviolet circular dichroic spectrum of corticotropin and comparison of the rotational strengths of the phenylalanyl and tyrosyl bands reveals no evidence for increased rotational freedom in 6M guanidinium hydrochloride. Spectral changes are observed, however, in the transitions arising from the single tryptophan. This study suggests that corticotropin in aqueous solution may serve as a better model for the circular dichroic spectrum of the aperiodic regions in globular proteins than either synthetic homopolypeptides or reference proteins for which spectral and X‐ray diffraction data are available.
Binding of proflavin to T2L bacteriophage and its DNA
Authors: McCall Philip J. , Bloomfield Victor A. 
Published: December 2004

AbstractWe have measured the binding equilibria of proflavin to T2L bacteriophage, in both “slow” and “fast” sedimenting forms, and to free T2L DNA. Measurements were carried out by difference spectroscopy at 430 nm at temperatures from 13 to 43°C and at pH 5.6 and 7.6. We found no significant difference in the binding parameters of the two phage forms. Also, the fraction of nucleotides available as binding sites for proflavin was the same for both free and intraphage DNA. However, the binding constant is about an order of magnitude lower for encapsulated than for free T2L DNA, due to the decreased exothermicity of the binding reaction within the phage head.
Electric mobility of bivalent cations in the presence of an anionic polysaccharide
Authors: Magdelénat H. , Turq P. , Chemla M. , Para B. 
Published: December 2004

AbstractThe electrophoretic mobilities of bivalent cations (Ca++ and Sr++) were measured in the presence of a linear anionic polysaccharide extracted from cartilage—chondroitin sulfate. The experimental results were analyzed according to Manning's treatment which involves only the charge‐density parameter ξ related to the structure of the polyion and the charge of the counterion. The comparison between the electrophoretic mobility and the self‐diffusion coefficient enabled us to determine the apparent charge of the counterions in the different domains of concentration.
On the application of polyelectrolyte limiting laws to the helix–coil transition of DNA. IV. Dependence of helix stability on the concentration of divalent metal ions
Authors: De Marky Nancy , Manning Gerald S. 
Published: December 2004

AbstractThe molecular theory of the previous paper in this series is extended to determine the effect of divalent metal ions on helix stability relative to coil at fixed ionic strength and nucleotide phosphate concentration. Specification of the state of condensed counterions, as well as their concentration, is essential for the solution of this problem, and it is assumed that they translate freely within a thin cylindrical shell close to the polynucleotide. As a function of divalent counterion concentration m the relative stability of the helix is highly nonlinear. Although the overall trend is that the helix stability increases with addition of divalent metal ion, there is a narrow concentration range for which it decreases slightly. The behavior of the relative stability as a function of m is determined by the translational degrees of freedom of the counterions, both univalent and divalent, both condensed and uncondensed. Detailed comparison of the theory with data is not given here, but it is pointed out that the calculated values of the relative stability are consistent with the order of magnitude of the observed effect Mg2+ on the melting temperature.
Proton and phosphorus nmr studies of d‐CpG(pCpG)n duplexes in solution. Helix–coil transition and complex formation with actinomycin‐D
Authors: Patel Dinshaw J. 
Published: December 2004

AbstractThe Watson–Crick imino and amino exchangeable protons, the nonexchangeable base and sugar protons, and the backbone phosphates for d‐CpG(pCpG)n, n = 1 and 2, have been monitored by high‐resolution nmr spectroscopy in aqueous solution over the temperature range 0°–90°C. The temperature dependence of the chemical shifts of the tetramer and hexamer resonances is consistent with the formation of stable duplexes at low temperature in solution. Comparison of the spectral characteristics of the tetranucleotide with those of the hexanucleotide with temperature permits the differentiation and assignment of the cytosine proton resonances on base pairs located at the end of the helix from those in an interior position. There is fraying at the terminal base pairs in the tetranucleotide and hexanucleotide duplexes. The Watson–Crick ring imino protons exchange at a faster rate than the Watson–Crick side‐chain amino protons, with exchange occurring by transient opening of the double helix. The structure of the d‐CpG(pCpG)n double helices has been probed by proton relaxation time measurements, sugar proton coupling constants, and the proton chemical shift changes associated with the helix–coil transition. The experimental data support a structural model in solution, which incorporates an anti conformation about the glycosyl bonds, C(3) exo sugar ring pucker, and base overlap geometries similar to the B‐DNA helix. Rotational correlation times of 1.7 and 0.9 × 10−9 sec have been computed for the hexanucleotide and tetranucleotide duplexes in 0.1 M salt, D2O, pH 6.25 at 27°C. The well‐resolved 31P resonances for the internucleotide phosphates of the tetramer and hexamer sequences at superconducting fields shift upfield by 0.2–0.5 ppm on helix formation. These shifts reflect a conformational change about the ω,ω′ phosphodiester bonds from gauche‐gauche in the duplex structure to a distribution of gauche‐trans states in the coil structure. Significant differences are observed in the transition width and midpoint of the chemical shift versus temperature profiles plotted in differentiated form for the various base and sugar proton and internucleotide phosphorous resonances monitoring the d‐CpG(pCpG)n helix–coil transition. The twofold symmetry of the d‐CpGpCpG duplex is removed on complex formation with the antibiotic actinomycin‐D. Two phosphorous resonances are shifted downfield by ∼2.6 ppm and ∼1.6 ppm on formation of the 1:2 Act‐D:d‐CpGpCpG complex in solution. Model studies on binding of the antibiotic to dinucleotides of varying sequence indicate that intercalation of the actinomycin‐D occurs at the GpC site in the d‐CpGpCpG duplex and that the magnitude of the downfield shifts reflects strain at the O‐P‐O backbone angles and hydrogen bonding between the phenoxazone and the phosphate oxygens. Actinomycin‐D is known to bind to nucleic acids that exhibit a B‐DNA conformation; this suggests that the d‐CpG(pCpG)n duplexes exhibit a B‐DNA conformation in solution.
ESR investigation of the binding of acidic biopolymers to synthetic apatite
Authors: Peckauskas R. A. , Termine J. D. , Pullman I. 
Published: December 2004

AbstractThe interaction between synthetic crystalline calcium phosphate (apatite) and acidic macromolecules (sodium polyacrylate, sodium poly(L‐glutamate), chondroitin sulfate, phosvitin) was investigated by electron spin resonance spectroscopy of mineral‐macromolecule complexes doped with vanadyl ion (VO++) as a paramagnetic probe. Changes in magnetic parameters were interpreted in terms of bonding between mineral and macromolecule. The VO++ probe data indicated that polymer acidic functional groups were bound to mineral surfaces in all cases.
Infrared spectra and resonance interaction of amide‐I vibration of the parallel‐chain pleated sheet
Authors: Chirgadze Yu. N. , Nevskaya N. A. 
Published: December 2004

AbstractResonance vibrational interactions of amide I for the parallel‐chain pleated‐sheet structure have been treated on the basis of the perturbation theory in a dipole–dipole approximation. The infinite sheet and finite fragments of different types have been considered. The possibility of experimental observation by infrared spectra of parallel‐chain pleated‐sheet fragments in globular proteins is discussed.
Infrared spectra and resonance interactions of amide‐I and II vibrations of α‐helix
Authors: Nevskaya N. A. , Chirgadze Yu. N. 
Published: December 2004

AbstractAmide‐I and II vibrations of α‐helix have been treated on the basis of the perturbation theory in a dipole–dipole approximation. The infinite helix and its finite fragments have been considered as models. The calculated infrared spectra for the infinite helix are in good agreement with the spectra of synthetic polypeptides. In the case of finite fragments of the α‐helix, the characteristic contours of the amide‐I and II bands appear when the nuimber of peptide groups is about 10 and 6, respectively.
Electron diffraction of Valonia cellulose. A quantitative interpretation
Authors: Claffey W. , Blackwell J. 
Published: December 2004

AbstractThe crystal structure of native cellulose (Valonia) has been analyzed by electron diffraction. Possible models for the structure were refined by rigid‐body least squares methods, which incorporated parameters defining the preferred orientation of the fibrils around their long axes in the cell wall lamellae. The structure was found to consist of an array of chains having the same sense (i.e., parallel), with packing parameters similar to those recently determined by X‐ray diffraction. The eight‐chain unit cell could be approximated adequately by a two‐chain monoclinic unit cell with dimensions a = 8.18 Å, b = 7.84 Å, c = 10.38 Å (fiber axis), and γ = 97.04°; the space group is P21.
Raman spectroscopic study of the proteins of egg white
Authors: Painter P. C. , Koenig J. L. 
Published: December 2004

AbstractThe Raman spectra of ovalbumin, ovomucoid, and conalbumin are reported. Spectral shifts in the conformationally sensitive amide I and amide III lines as a result of thermal denaturation indicate the formation of intermolecular β‐ sheets. A medium intensity line at 1260 cm−1 in the spectra of ovomucoid and ribonuclease is demonstrated to contain a substantial contribution from tyrosine residues.
Dynamic light scattering from collagen solutions. I. Translational diffusion coefficient and aggregation effects
Authors: Fletcher Guy C. 
Published: December 2004

AbstractSolutions of native collagen extracted from rat tail tendons in neutral salt solution have been studied by dynamic light scattering. The spectra obtained are consistent with the presence in solution of both single rod‐shaped collagen molecules and aggregates of molecules. No contribution to the spectrum has been detected at any scattering angle from rotational diffusion of single molecules, although a measurable broadening effect is expected at high angles. The translational diffusion coefficient D of single molecules, calculated from the broader spectral component, shows an anomalous dependence on collagen concentration with a maximum value of D20,w = 8.6 ± 0.2 × 10−12 m2/sec near the concentration 0.04% by weight. Above 0.05% D falls linearly with increasing concentration and takes the value D 20,w = 8.1 ± 0.2 × 10−12 m2/sec at 0.064% collagen.
Investigation of the formation of triple helices between (pro‐pro‐gly)n's of different degrees of polymerization using gel filtration
Authors: Kobayashi Yuji , Suezaki Yukio , Inouye Katsuhiko , Tanaka Kaori , Kakiuchi Kinji , Kyogoku Yoshimasa 
Published: December 2004

AbstractThe properties of triple‐helix formation of (Pro‐Pro‐Gly)n were studied. The probability of hybridization between the polytripeptides (Pro‐Pro‐Gly)n, of different degrees of polymerization was investigated by gel filtrations of mixed solutions of them. Using samples selectively labeled with radioactivity, the elution pattern was detected by uv absorption and liquid scintillation counting. The hybridization was found only when the difference of polymerization is small. The amount of heterohelices (triple helices of the polypeptide chains with different degrees of polymerization) measured by integrated intensity of elution pattern was comparable to the theoretical value of Suezaki and Go. Concentration dependence of the helix–coil transition temperature of (Pro‐Pro‐Gly)n was also measured by the use of optical rotation and discussed with the theoretically expected values.
Kinetic analysis of the annealing period in the formation of the poly(A)·2poly(U) triple helix
Authors: Spodheim Melanie , Neumann Eberhard 
Published: December 2004

AbstractThe slow kinetics of annealing processes in multistranded nucleic acids is spectrophotometrically investigated using poly(A)·2poly(U) as a model system. The absorbance changes at specific wavelengths show that double‐helical (A·U) base pairs appear as transient intermediates. The annealing process is identified by the enlargement of triple‐helical sequences at the cost of (A·U) base pairs and unpaired (U) residues. A large time range in the reorganization of mismatched chain configurations is characterized by a logarithmic dependence on time. This observation is quantitatively described by a kinetic model developed by Jackson. In Jackson's model the rate‐limiting process in the slow annealing phase of maximizing triple‐helical sequences, is the removal of strand entanglements, knots, and hairpin loops by complete unwinding of those helical stretches which stabilize the mismatched configurations. The results of the present study are briefly discussed in terms of optimum conditions for hybridization experiments and for the preparation of polynucleotide complexes commonly used to produce interferons.
Conformational behavior of polyethylenimine derivatives revealed by fluorescence spectroscopy
Authors: Pranis Robert A. , Klotz Irving M. 
Published: December 2004

AbstractConformation behavior of polyethylenimine has been examined by studies of the fluorescence characteristics of derivatives of the polymer containing pyrenyl ligands. Excimer formation within the macromolecular matrix serves as a sensitive probe of group proximities. The experimental observations combined with nearest neighbor analyses lead to quantitative assessments of the extent of interaction between polymer side chains.
An X‐ray diffraction study of poly(L‐lysine hydrobromide)
Authors: Suwalsky M. , Llanos A. 
Published: December 2004

AbstractA structural study of the synthetic polypeptide poly(L‐lysine hydrobromide) has been made by X‐ray fiber techniques. The investigation was undertaken to determine whelther this polymer undergoes conformational transitions as a function of hydration in a manner similar to other chemically related basic polypeptides. Specifically, a comparison with the previously reported structures of the hydrochloride form of poly(L‐lysine) was sought. Homogeneous powder mixtures with various amounts of water and oriented fibers of poly(L‐lysine hydrobromide) at different relative humidities were X‐ray photographed. Reversible transitions amorphous state ⇌ β‐pleated sheet ⇌ α‐helix ⇌ isotropic solution as a function of increasing/decreasing degrees of hydration were found. The β‐pleated‐sheet conformation was observed between 33% and 76% relative humidities (containing about one and three molecules of water per residue, respectively). Each pleated sheet was formed by “antiparallel” chains, and the sheets were piled up along the b‐axis. The spacings of this conformation did not vary appreciably with hydration. The observed reflections at 52% relative humidity (1.4 molecules of water per residue) could be indexed satisfactorily in terms of an orthorhombic unit cell, of space group P21221, with a = 9.52 Å, b = 16.44 Å, and c = 6.80 Å. These dimensions were shown by models to be compatible with the proposed structure. The α‐helix conformation was present in specimens photographed at 76% relative humidity and up, and containing between three and fifteen molecules of water per residue. The helices were packed parallel to each other in a hexagonal array but randomly along or about their lengths. Increasing the hydration from five to fifteen molecules of water per residue causes the a‐axis to increase from 16.9 to 20.8 Å. Twenty molecules of water per residue produced an isotropic solution. Despite some structural differences between the hydrobromide and hydrochloride forms it is concluded that the role played by the anions is mainly related to determining the water content levels at which conformational changes occur. Therefore, the anions do not significantly influence the prevailing conformation in this particular system, but might affect the packing arrangement of the polypeptide chains.
Synthesis of linear stereoregular glucomannan heteropolysaccharides
Authors: Kobayashi Kazukiyo , Eby Ronald , Schuerch Conrad 
Published: December 2004

AbstractA series of stereoregular α‐(1 → 6) linked glucomannans have been prepared by Lewis acid‐catalyzed copolymerization of anhydro sugar derivatives followed by debenzylation. The products have been characterized for mole fraction of the individual monomer, and sequence lengths have been calculated from copolymerization data. The viscosity, specific rotation, and 13C nmr spectra have been correlated with the structure of the various copolymers.
Co‐oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. VI. Circular dichroism studies of co‐oligopeptides of L‐phenylalanine, L‐tryptophan, and glycine
Authors: Rizzo Vincenzo , Luisi Pier Luigi , Straub Barbara , Guarnaccia Rocco 
Published: December 2004

AbstractThe circular dichroic properties of H‐Gly‐Phe‐(Gly)n‐Trp‐Gly‐OH (II, n = 0,1,2) and of related simpler peptides, such as H‐Phe‐Gly‐OH, H‐Gly‐Phe‐OH, H‐Gly‐Phe‐Gly‐OH, H‐Phe‐Trp‐OH, H‐Phe‐Trp‐Gly‐OH, and H‐Gly‐Phe‐Trp‐OH in water and trifluoroethanol solutions are investigated. Peptides containing only one phenylalanyl residue show markedly different near‐uv dichroic signals depending on whether this residue is in the N‐terminal position or not. The possible origin of this feature is discussed. The study of the oligopeptides II (n = 0,1,2) shows that no strong intramolecular interaction between the two aromatic rings is present. However, the dichroic properties of II (n = 0) are clearly anomalous, and the analysis of H‐Gly‐Phe‐Trp‐OH, H‐Phe‐Trp‐Gly‐OH, and of H‐Phe‐Trp‐OH at different pH's, confirms that the presence of two adjacent aromatic residues may bring about chiroptical properties which indicate a restriction in the conformational equilibrium of the molecule. The limits, and the possible generalization of this finding, are discussed.
Theory of protein molecule self‐organization. III. A calculating method for the probabilities of the secondary structure formation in an unfolded polypeptide chain
Authors: Finkelstein A. V. 
Published: December 2004

AbstractA mathematical model is developed adequately describing an unfolded polypeptide chain without long‐range interactions in which fluctuating hydrogen‐bonded α‐helices, β‐bends, fragments of helices 310, and other local structures are formed. The obtained model is a modification of a one‐dimensional Ising model for a heteropolymer and allows one to determine the probability of formation of different secondary structures in various parts of a polypeptide chain, provided the whole set of structural thermodynamic parameters exists.
Dynamic light‐scattering studies of DNA. I. The coupling of internal modes with anisotropic translational diffusion in congested solutions
Authors: Lee Wylie I. , Schmitz Kenneth S. , Lin Sung‐Chang , Schurr J. Michael 
Published: December 2004

AbstractA model for the coupling between internal modes, or molecular rotation, and anisotropic translational diffusion in congested solutions is proposed to account for the anomalously slow component that has appeared ubiquitously in reported autocorrelation functions of Rayleigh scattered light from solutions of DNA's with molecular weights greater than about 107. The predicted existence of an anomalously slow mode in addition to a faster “normal” mode, as well as the predicted relative amplitudes of both fast and slow components, are qualitatively in agreement with the observations. For sufficiently long‐wavelength fluctuations all of the amplitude appears in the slower mode, which then exhibits an appropriately averaged translational diffusion coefficient.In support of the model it is shown in the Appendix that nonideal central interactions between macromolecules are by themselves insufficient to generate isolated internal mode relaxation terms in the autocorrelation function, unless translational ordering of the macromolecules extends over the illuminated observation region.
Nuclear magnetic resonance studies of exchangeable protons. II. The solvent exchange rate of the indole nitrogen proton of tryptophan derivatives
Authors: Waelder Susan F. , Redfield Alfred G. 
Published: December 2004

AbstractThe exchange rate of the indole nitrogen proton with solvent water protons was measured as a function of pH and temperature for tryptophan, N‐methyl tryptophan, glycyl tryptophan, tryptophanamide, tryptophylglycine, and tryptophylglycyl glycine. The nmr observation was by long‐pulse Fourier transform methods, and kinetics were inferred from saturation recovery, H2O transfer of saturation, and linewidth. There are observable differences between the rates of these compounds, but all are describable within a factor of two by specific acid and base‐catalyzed rates kH = 100 and kOH = 108 1/mol‐sec at 27°C. It is concluded that this behaviour is representative of this proton on the indole side chain in a random‐chain peptide exposed to water.
Stable and metastable forms of poly(G)
Authors: Howard F. B. , Frazier J. , Miles H. Todd 
Published: December 2004

AbstractPoly(G) is shown by ir spectroscopy to be capable of existence in a metastable form which is converted spontaneously at ambient temperature, or more rapidly on heating, to a stable form. The metastable form can be regenerated by freezing and thawing the solution.The high‐charge density of four‐stranded poly(G) makes it especially susceptible to electrostatic destabilization by use of Et4N+ counterions, which screen electrostatic repulsion of multiple strands less effectively than alkali metal ions. Poly(G) has been obtained for the first time in the single‐stranded form in aqueous solution and shown to undergo a fully reversible helix–coil transition on heating.