bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformation and aggregation of melittin: Effect of pH and concentration of sodium dodecyl sulfate
Authors: Kubota Shigeo , Yang Jen Tsi 
Published: December 2004

AbstractThe conformation of melittin, a surface‐active polypeptide, in solution was studied by CD spectra between 190 and 240 nm. The molecule was essentially unordered (possibly with a trace of helix) in water without salt at neutral pH. Upon deprotonation of four of the six cationic groups at pH 12 the polypeptide became partially helical (about 35%). The addition of NaDodSO4 to an aqueous melittin solution first caused the solution to become turbid but it became clear again in excess surfactant solution. The conformational changes depended on the molar NaDodSO4/melittin ratio, R. With R from 2.34 to 23.4, the melittin solution was turbid and the polypeptide conformation was probably a mixture of α‐helix and β‐sheets. This was supported by the ir spectrum of the turbid solution, which indicated the presence of both conformations. With R = 46.8 or 468 (1 or 10 mM NaDodSO4) the polypeptide conformation was characteristic of an α‐helix, about 70–80% of the molecule, regardless of whether the surfactant was above or below its critical micelle concentration. This compared well with the x‐ray results of 92% helix in crystals. The lower helicity of melittin in NaDodSO4 solution might be attributed to the end effects that destabilize the first and last turn of an helix at its N‐ and C‐terminus, respectively.
Rate constants and activation parameters for the mobility of bulk and DNA‐associated glycol–water solvents
Authors: Milton John G. , Galley William C. 
Published: December 2004

AbstractThe decrease in mobility of viscous glycol–water solvents when associated with native DNA is quantified from a study of the loss of the exciting‐wavelength dependence of the phosphorescence spectrum of free and bound proflavin with increasing temperature. The data are interpreted in terms of a distribution of rate constants with an Arrhenius temperature dependence. Over the temperature range of the experiments a relative decrease of ∼ 104 in the average rate constant is observed for reorientation of the solvent when associated with DNA. The basis for this large reduction is found to derive from a large decrease in the pre‐exponential factors (i.e., activation entropy) associated with the reorientation rate constants. The changes in the distribution of rate constants and the activation parameters for solvent mobility induced by DNA do not resemble the changes observed for any one of a number of small ion or molecule perturbations. The results suggest the presence of disorganized, relatively immobile solvent in association with DNA.
A positron annihilation study of hydrated DNA
Authors: Warman John M. , Eldrup M. 
Published: December 2004

AbstractPositron annihilation measurements are reported for hydrated DNA as a function of water content and as a function of temperature (20 to −180°C) for samples containing 10 and 50% wt of water. The ortho‐positronium mean lifetime and its intensity show distinct variations with the degree of hydration and with temperature for the 50% sample. The 10% water sample was relatively insensitive to temperature variation. The results indicate that hydrated DNA containing up to 10% water behaves as a rigid crystalline solid but that the rigidity markedly decreases with a further increase in water content until, for approximately 50% water, its properties resemble more those of a highly viscous fluid.
Scaled particle theory applied to gels of high molecular weight DNA in the ultracentrifuge
Authors: Richard Alfred J. , Westkaemper Richard B. 
Published: December 2004

AbstractEquilibrium ultracentrifugation of high molecular weight DNA at moderate centrifuge speed leads to the formation of gel at the bottom of the centrifuge cell. The swelling pressures of the gels are strongly affected by the ionic strength of the medium and by polyvalent counterions in the medium. Scaled particle theory applied to the DNA gels gives values to the effective particle length and particle radius of the DNA. Different models for DNA conformations in the gels were required for the monovalent, the divalent, and the tetravalent cations used in this study.
ψ Compaction of poly[d(AT)] · poly[d(AT)]
Authors: Shin Yong A. , Feroli Susan L. , Eichhorn Gunther L. 
Published: December 2004

AbstractThe compaction of poly[d(A–T)] · poly[d(A–T)] by Co(III) is accompanied by the formation of ψ(+)‐ and ψ(‐)‐structures. The chirality of the ψ‐structure depends on the Co(III) concentration, ionic strength, temperature, pH, and the chain length of the polymer. The two forms can be readily interconverted by manipulating these factors. Phase diagrams have been constructed that demonstrate the regions of stability of the enantiomers as a function of two variables, while other factors are held constant. At critical points in the phase diagram the two forms are in such unstable equilibrium that mechanical motion will cause ψ(+) ⇆ ψ(‐) interconversion. The formation of both ψ(+)‐ and ψ(‐)‐structures by the action of Co(III) on poly[d(A–T)] · poly[d(A–T)] contrasts markedly with the behavior of poly[d(G–C)] · poly[d(G–C)] in similar circumstances by forming only the ψ(+)‐structure and that of native DNA to produce no ψ at all. Thus the base sequence is important in determining the structure of chirally associated DNA molecules.
Helix → β conformational transition of poly(L‐lysine) on dye binding
Authors: Scaria P. V. , Atreyi M. , Rao M. V. R. 
Published: December 2004

AbstractBinding of an azo dye, 4′‐dimethyl amino azo benzene‐4‐carboxylic acid (DAAC) to poly(L‐lysine) (PLL) in basic aqueous solutions at 20°C has been studied. The azo dye was found to bind to PLL when its side‐chain amino groups are in the uncharged state. This was found to be a cooperative phenomenon, and the binding constant and cooperativity factor have been evaluated. The binding of the dye was found to result in a conformational transition of PLL from the α‐helix to the β‐sheet, which in turn helps in increased dye binding.
Local sequence patterns of hydrophobicity and solvent accessibility in soluble globular proteins
Authors: Lipman David J. , Pastor Richard W. , Lee B. 
Published: December 2004

AbstractWe examined the variation in the solvent accessibility and hydrophobicity of the amino acids along the sequences of 58 soluble globular proteins with known tertiary structure. We found that there is a significant tendency for the accessibilities to run in clusters along the sequence but that the hydrophobicities are distributed without such nonrandom clusters. Theseresults suggest severe limitations on the power of sequence analysis tools that use average hydrophobicity scores of overlapping subsequences to predict accessibility.
A model of the hydrodynamic behavior of irradiated DNA: Dependence on molecular conformation
Authors: Ostashevsky Joseph Y. , Lange Christopher S. 
Published: December 2004

AbstractThe model presented here describes the DNA viscosity and viscoelastometric responses to ionizing radiation‐induced molecular breakdown. Four DNA conformations are considered: (1) linear chain, (2) relaxed circle, (3) supercoiled circle, and (4) supercoiled linear. The model includes the systems of differential equations for calculating the size distributions of DNA molecules as functions of dose. Thedistributions are used in the usual hydrodynamic formulae for heterogeneouspopulations of polymer molecules. The sensitivity of viscoelastometry for the estimation of D37 is better than that of viscometry. The model predicts a considerable difference between the radiation responsesof linear and circular DNAs. The prediction is confirmed by experimental data for T4 DNA [C. S. Lange et al. (1984) Rad. Res. 100, 1–15] and E. coli DNA [S. E. Bresler et al. (1984) Biophys. J. 45, 749–754]. Thus, ionizing radiation can be used to determine the original conformation of DNA molecules.
Solid‐state conformations of α‐Aminoisobutyryl‐L‐prolyl sequences: Crystal structure of Boc‐Aib‐L‐Pro‐OBzl
Authors: Kawai Masao , Butsugan Yasuo , Fukuyama Keiichi , Taga Tooru 
Published: December 2004

AbstractThe protected dipeptide Boc‐Aib‐Pro‐OBzl, C21H30N2O5, crystallizes in the orthorhombic space group P212121, with a = 12.820, b = 10.529, c = 16.548Å, and Z = 4. The crystal structure has been solved by direct methods and refined to an R value of 0.074 for 1352 reflections. The Boc‐Aib‐Pro‐OBzl molecule has been shown to adopt an unfolded conformation in the solid state with ϕAib = 50.5°, ΨAib = 45.3°, ϕPro = −64.6°, and ΨPro = 148.1°. The result is in marked contrast with the reported crystal structure of Cbz‐Aib‐Pro‐NHMe, which adopts an intramolecularly hydrogen‐bonded β‐turn conformation. Comparison with 13 reported conformations of Aib‐Pro sequences in the crystalline state revealed that the Aib‐Pro sequence adopts an unfolded conformation if the residue that immediately follows the dipeptide sequence possesses no hydrogen available for hydrogen bonding, while a β‐turn conformation is preferred if the Pro residue is followed by an NH group. Correlation between pyrrolidine ring puckering of the Pro residue and main‐chain conformation in Aib‐Pro sequences is discussed.
On the CD helix band for long helical polymers
Authors: Rabenold David A. , Rhodes William 
Published: December 2004

AbstractThe CD helix bands for infinitely long helical polymers are shown tobe composed of two parts: a derivative‐shaped band plus an ordinary Gaussian‐like band. The derivative‐shaped band results from the zero‐order term of an expansion while the Gaussian‐like band results from the first‐order expansion term. However, the intensities of the two bands are shown to be of the same order of magnitude. They are both linear in the coulombic coupling of transition charge densities for polymer transitions. The sum yields a skewed derivative‐shaped band. The shapes of net CD helix bands are shown to not depend on the approximations used for averaging over orientations if the usual systems, such as polypeptides and polynucleotides, are considered in their long‐wave‐length spectral regions.
Vibrational spectroscopic analysis of LD‐sequential, bacterial cell wall peptides: An IR and raman study
Authors: Naumann Dieter , Labischinski Harald , Rönspeck Wolfgang , Barnickel Gerhard , Bradaczek Hans 
Published: December 2004

AbstractThe synthetic, zwitterionic bacterial cell wall peptides—D‐Gluγ‐L‐Lys, D‐Gluγ‐L‐Lys‐D‐Ala, D‐Gluγ‐L‐Lys‐D‐Ala‐D‐Ala, and L‐Ala‐D‐Gluγ‐L‐Lys‐D‐Ala‐D‐Ala—have been investigated in the crystalline and aqueous solution state applying ir and Raman spectroscopy. Additionally, aqueous solutions of the tetra‐ and pentapeptide have been investigated by CD spectroscopic techniques. Apart from the dipeptide, whose spectral features were dominated by end‐group vibrations, the corresponding ir and Raman active bands of the crystalline peptides in the amide and skeletal regions were found at similar wave numbers, thus suggesting an analogous three‐dimensional structure of these compounds. Dominant amide A, I, II, and III bands near 3275, 1630, 1540, and 1220–1250 cm−1, respectively, in the ir are interpreted in favor of an intermolecularly hydrogen‐bonded, β‐like structure. The absence of any amide components near 1680–1690 cm−1, together with the presence of strong amide bands near 1630 cm−1, and weak bands near 1660 cm−1 in the ir, which, conversely, were found in the Raman spectra as weak and strong bands, but at corresponding wave numbers, is taken as strong evidence for the presence of the unusual, parallel‐arranged β‐structure. On the basis of comparative theoretical considerations, a parallel‐arranged, “β‐type ring” conformation [P. De Santis, S. Morosetti, and R. Rizzo (1974) Macromolecules 7, 52–58] is hypothesized. The solubilized peptides exhibited distinct similarities with their crystalline counterparts in respect to frequency values and relative intensities of the corresponding ir and Raman‐active amide I/I′ components, and of some Raman bands in the skeletal region. This is interpreted in terms of residual short‐range order, persisting even in aqueous solution. We concluded that the peptides show a strong propensity to form hydrated, strongly associated aggregates in water. On the basis of amide I/I′ band positions, stable, intramolecular interactions via the amide groups are discarded for the solubilized peptides. Complementarily, the CD data obtained suggest the presence of weakly bent, “open‐turn”‐like structures for the tetra‐ and pentapeptide in aqueous solution.
Dynamic properties of oxy‐ and carbonmonoxyhemoglobin probed by optical spectroscopy in the temperature range of 300–20 K
Authors: Leone Maurizio , Cupane Antonio , Vitrano Eugenio , Cordone Lorenzo 
Published: December 2004

AbstractWe have studied the absorption bands of oxy‐ and carbonmonoxyhemoglobin in the wavelength range of 650–350 nm (visible and Soret bands) and in the temperature range of 300–20 K. The spectra in the whole temperature range have been successfully deconvoluted in terms of gaussian components. The analysis of the temperature dependence of the first and second moment of the bands enables us to compare dynamic properties of the heme group in oxy‐ and carbonmonoxyhemoglobin. The results of the analysis indicate that the “mean‐effective” frequency of the nuclear motion coupled to the electronic transition responsible for the visible bands is higher in carbonmonoxy‐ than in oxyhemoglobin. The possible functional relevance of this finding is discussed.
CD studies of synthetic polypeptides as histone models: Poly(L‐Arg‐L‐Ile‐Gly), poly(L‐Arg‐L‐Nva‐Gly), and poly(L‐Arg‐L‐Nle‐Gly)
Authors: Tsikaris Vassilios , Sakarellos‐Daitsiotis Maria , Sakarellos Constantinos , Marraud Michel 
Published: December 2004

AbstractSequential polypeptides (L‐Arg‐X‐Gly)n were prepared as synthetic models of arginine‐rich histones to study their structure and their stereospecific interactions with DNA. In our previous work the conformational characteristics of poly(L‐Arg‐L‐Ala‐Gly), poly(L‐Arg‐L‐Val‐Gly), and poly(L‐Arg‐L‐Leu‐Gly) have already been analyzed. To obtain further insight into the influence of the X residue side chain on the conformation of the (L‐Arg‐X‐Gly)n polytripeptides, we now report their synthesis and cd properties when X represents the amino acid residues Ile, Nva, and Nle. The pentachlorophenyl active esters of the appropriate tripeptides were used to perform the polymerization, and the toluene‐4‐sulfonyl group was used to protect the arginine guanido group. CD spectroscopy showed that, in 100% trifluoroethanol, the degree of helical conformation increased in the order Ile → Nle → Nva. An equilibrium between β‐turn, α‐helix, and random‐coil conformers occurred in 100% hexafluoroisopropyl alcohol, while a rise in the temperature or the addition of water favored the α‐helix, the highest percentage of which was observed in a mixture of hexafluoroisopropyl alcohol: water (20 : 80) and in the order Ile → Nle → Nva. In aqueous solutions (at pH 7 and 12) the polymers behaved as a random coil, but they were forced to a less aperiodic structure, over a range of ionic strengths (0–0.5M NaF). A rise in temperature of up to 70°C in 100% trifluoroethanol resulted in a decrease of the α‐helix percentage of the polymers, while in aqueous solutions the aperiodic structure decreased with increasing temperature. This study proved the importance of the nature of the X residue (length, Cβ branching) in relation to the structural order of the sequential polypeptides. We concluded that the polymers prepared are suitable models for arginine‐rich histones.
Helical formation of a 13‐residue C‐peptide analogue of ribonuclease a in sodium dodecyl sulfate solution
Authors: Wu Chuen‐Shang C. , Yang Jen Tsi 
Published: December 2004

AbstractThe conformation of a 13‐residue C‐peptide analogue of ribonuclease A——in surfactant solutions was studied by CD. The CD spectrum of the peptide in excess NaDodSO4 solution was typical for a helical conformation; the spectrum appeared to be virtually independent of pH (2.5–6) and temperature (3–25°C). Analysis of the CD data indicated a helicity of about 65–70% with no α‐sheet and β‐turn; this corresponded to 8 or 9 residues in the helical form or slightly more than two turns of α‐helix. This compares with an average of about one turn of α‐helix for the C‐peptide analogue in water at pH 4.7 and 7°C. The conformation of the peptide in cationic surfactant, dodecyl ammonium chloride, and nonionic surfactant, dodecyl heptaoxyethylene ether, solution resembled that in water. We concluded that the C‐peptide analogue can develop a maximum helicity close to the corresponding segment in ribonuclease A in hydrophobic environment provided by the clustering of NaDodSO4 molecules to the cationic side groups of the peptide, except that the end effects may destabilize two or three residues each at both ends of the helix. Thus, in the interior of a protein molecule this hydrophobic effect may overshadow the charged‐group effect than can be explained by the helix dipole model for the helical segments on the exterior of the protein molecule.
Polarized raman scattering from oriented single microcrystals of d(A5T5)2 and d(pTpT)
Authors: Patapoff Thomas W. , Thomas Gerald A. , Wang Yang , Peticolas Warner L. 
Published: December 2004

AbstractPolarized Raman spectra have been obtained from single microcrystals of the duplex of the decamer d(A5T5)2 using a Raman microscope. This is the first report of Raman spectra from a crystal of a deoxyoligomer that contains only long, nonalternating sequences of adenine and thymine. Sequences containing d(A)n and d(T)n are of interest in view of recent suggestions that they induce bends in DNA and that they might exist in a nonstandard B‐conformation. Polarized Raman spectra of a crystal of d(pTpT) have also been obtained. Both crystals display Raman bands whose intensities are very sensitive to the orientation of the crystal with respect to the direction of polarization of the incident laser beam. These spectra indicate that the helical axes of the oligonucleotides are parallel to the long axes of the crystals and that the d(A5T5)2 is not appreciably bent in the crystal. The Raman spectrum from the d(pTpT) crystal indicates that all of the furanose ring puckers are in a C2′‐endo configuration since only the C2′‐endo marker band at 835 ± 5 cm−1 is present. Crystals of d(A5T5)2 show measurable Raman intensities in both the 838‐ and 816‐cm−1 bands. This indicates the presence of both the C2′‐endo and C3′‐endo, or possibly other non‐C2′‐endo, furanose conformations. The 816‐cm−1 band is weak so that only a small fraction of the residues are estimated to be in the non‐C2′‐endo conformation. In both the d(pTpT) and d(A5T5)2 crystals the intensity of the bands due to vibrations of the backbone show only a small dependence on orientation of the crystals. This result is explained by the low symmetry of the puckered sugar rings. It is concluded that Raman spectra obtained from oligonucleotide crystals in which the orientation of the crystal axes to the laser polarization is not carefully controlled may contain intensity artifacts that are due to polarization effects.
A 2H‐nmr study of the DNA hydration water in solid li‐DNA assemblies
Authors: Brandes Rolf , Kearns David R. , Rupprecht Allan 
Published: December 2004

AbstractHigh‐resolution 2H‐nmr is employed to monitor the D2O in hydrated solids of Li‐DNA prepared from solution by three different methods: lyophilization, slow evaporation of the water, and wet spinning in alcohol. From the spectral shapes and spin–spin relaxation measurements, the DNA in the lyophilized samples is found to be locally ordered with a domain size of ∼ 0.4 μm. Much longer range macrosopic ordering is found in samples prepared by slow evaporation of the water. Here the DNA spontaneously assembles into a structure that is probably cholesteric, in which the pitch axis is perpendicular to the plane on which the DNA dried. The wet‐spinning method produces macroscopically, uniaxially oriented DNA molecules with a maximum helix axis disorder of 12°. To aid in the comparison between calculated and experimental line shapes, a two‐dimensional technique is employed to separate the contributions to the line width arising from DNA static disorder, magnetic inhomogeneities, and spin–spin relaxation.
Structure–Activity relationship of tetrapeptides related to dermorphin: A 500‐MHz 1H‐nmr study
Authors: Castiglione‐Morelli M. A. , Tancredi T. , Trivellone E. , Balboni G. , Marastoni M. , Salvadori S. , Tomatis R. , Temussi P. A. 
Published: December 2004

AbstractSeveral tetrapeptide analogs of dermorphin have been studied by means of 1H‐nmr spectroscopy at 500 MHz in DMSO‐d6. In spite of the unfavorable properties of the solvent, it is possible to extract key structural information that, combined with the biological activity of the peptides, yields a structure–activity relationship that is consistent with our model of the μ receptor site. In particular, the importance of the orientation of the aromatic ring of the third residue, hypothesized in the theoretical model, is now substantiated. The shape of the P subsite of the receptor is also indirectly defined by the shape of several bulky side chains of the third residue.
Dynamic light‐scattering study of synthetic myosin filaments
Authors: Mochizuki‐Oda Noriko , Fujime Satoru 
Published: December 2004

AbstractSynthetic myosin filaments of rabbit were prepared. Electron microscopy showed that the number‐average length (Ln = 470 nm) and sharpness in length distribution (Lw/Ln = 1.036) were independent of ionic strengths of 134, 74, and 44 mM, whereas the number ratio of M‐filaments (about 15 nm in diameter at the bare zone) to m‐filaments (about 10 nm) strongly depended on ionic strength (IS); the major filaments were M‐filaments at IS = 134 mM, m‐filaments at IS = 74 mM, and almost exclusively m‐filaments at IS = 44 mM. Dynamic light scattering showed that the change in diameter with the change in ionic strength by 2‐h dialysis was reversible. Combination of dynamic light scattering and sedimentation studies suggested a dynamic equilibrium between M‐ and m‐filaments. Dynamic light‐scattering spectra at IS = 134 and 74 mM could be analyzed by a theory for rigid rods, whereas those at IS = 44 mM only by introducing semiflexibility of filaments; m‐filaments are more flexible at IS = 44 than at 74 mM.
The amplitude of local angular motions of intercalated dyes and bases in DNA
Authors: Schurr J. Michael , Fujimoto Bryant S. 
Published: December 2004

AbstractThe orientation of ethidium dye in DNA and the amplitude of its local internal angular motion are estimated from fluorescence polarization anisotropy and reduced linear dichroism data. When the local internal motion is assumed to be isotropic, the acceptable range of polar angles of the transition dipole is ϵ = 70°−72°, and the acceptable range of root mean squared (rms) amplitudes of local internal motion is 〈δϵ2〉1/2 = 6.9°–8°, in agreement with earlier estimates. The nmr relaxation data reported by Kearns and co‐workers for the imino protons of duplex (dAdT)26.5 and (dGdC)30 are analyzed using recent theoretical results for flexible filaments. For typical, or reasonable, assumed geometrical parameters, large rms amplitudes of local internal motion of the bases are not required to be superimposed on the collective motions due to twisting and bending deformations. For the particular geometrical parameters considered herein, rms amplitudes greater than about 12° are precluded by the data, but values as low as 0° are not. The low precision of present knowledge about solution structures does not allow a definitive statement about the rms amplitudes of local angular motion of the bases to be made independent of any structural or geometric assumptions.