bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic light scattering in a flow—a new method of particle anisotropy investigation
Authors: Lomakin A. V. , Noskin V. A. 
Published: December 2004

AbstractThis paper deals with the light scattering from particles rotating in a flow with a transverse velocity gradient. It is theoretically substantiated and experimentally proved that the scattered light spectrum contains reliable information of the particle configuration and dimensions. The proposed technique may prove also very promising for the analysis of particle polydispersion.
Monte carlo simulation of the solvent structure in crystals of a hydrated cyclic peptide
Authors: Hagler A. T. , Moult J. , Osguthorpe D. J. 
Published: December 2004

AbstractThe Monte Carlo simulation of the structure of the 16 ordered and disordered waters in the unit cell of crystals of the cyclic peptide cyclo(‐L‐Ala‐L‐Pro‐D‐Phe)2 is reported. The water structure has been characterized in terms of the statistically averaged positions of the individual molecules, their root‐mean‐square movements about these positions, the probability of finding a water in a given spatial position in the crystal (probability maps), and examination of individual configurations of the system. In this way a picture is obtained of the water structure, including water orientations (hydrogen positions), the hydrogen‐bonding network, and fluctuations in these structural features, to a degree hitherto unavailable either from experimental or theoretical studies. In addition, the variation in water structure in various peptide environments was studied and correlated with the energetics of the individual water molecules. Variations in the crystalline environment of different water molecules lead to energy differences of as much as 4–5 kcal/mol in their average energies. Similarly, differences are observed in the water–peptide and water–water components of the energy. Two different water potentials were tested. The results were compared with experimental data in terms of mean positions, root‐mean‐square movements, and the Fourier transform of the simulated water structure. The agreement factor (R factor) calculated from the theoretical water probability distribution was 18.8% compared to the x‐ray value of 14.5%, and the value of 28% when the water is omitted.
31P‐NMR studies of DNA in nucleosome core particles
Authors: Shindo Heisaburo , McGhee James D. , Cohen Jack S. 
Published: December 2004

Abstract31P Nmr parameters (δ, T1, W1/2, and NOE) were measured for the DNA in nucleosome core particles at three frequencies and compared with similar data for the histone‐free DNA. An essentially linear relationship was found between the frequency of observation and line‐width for the single broad envelope of 31P resonances of the DNA in the nucleosome cores. We attributed this largely to chemical shift dispersion, with smaller contributions from chemical shift anisotropy and dipolar broadening. These results suggest the presence of different environments for phosphorus atoms in the core particles. However, within the accuracy of the method, no asymmetry in the resonance could be detected, which would tend to rule out any significant degree of DNA “kinking.” To investigate the interactions of the DNA and histones within the core particles we also studied transitions induced by urea and by temperature. Urea caused two stepwise increases in linewidth, which we attributed to conformational changes. A biphasic transition was also observed in the temperature profile, consistent with previous optical studies [Weischet et. al. (1978) Nucleic Acids Res. 5, 139]. Various models with different types of local mobility were examined by the relaxation theory. A model of isotropic motion having a broad distribution of correlation times gave a fairly good fit to the 31P‐nmr data.
Reversion of the B to A transition of DNA induced by specific interaction with the oligopeptide distamycin A
Authors: Minchenkova L. , Zimmer Ch. 
Published: December 2004

AbstractThe effect of the DNA‐binding oligopeptide distamycin A on the B to A transition of DNA in ethanol/water solutions has been studied by means of CD. (The overbars indicate that it does not matter which particular form of the corresponding families is considered.) The results show that increasing the concentration of distamycin A reverses the A conformation (in 82% ethanol) to the B conformation due to its strong binding and stabilization of the latter. In accordance with previous data for pure aqueous solutions, a site size of 3.5 base pairs is obtained from the studies in water/ethanolic solutions. From the data on the B to A transition in the presence of distamycin A, we estimated the length of the cooperativity ν0 = 10 base pairs.The results demonstrate that the oligopeptide systems of distamycin, as well as those of netropsin, are effective stabilizers of the DNA B‐conformation.
Enzymatic depolymerization of lamellar single crystals of nigeran
Authors: Marchessault R. H. , Revol J.‐F. , Bobbitt T. F. , Nordin J. H. 
Published: December 2004

AbstractLamellar single crystals of the α‐glucan: nigeran have been subjected to controlled enzymic degradation as an approach to understanding polysaccharide organization in these crystals. Analysis of both reactant and products by various methods argues that a situation exists where the crystals are inaccessible at 20°C but become increasingly accessible as the temperature approaches that of solution for the crystals in water. One has to conclude that chain folds are inaccessible to enzymes at 20°C and become increasingly accessible as one approaches the “melting temperature.” This could be due to increased mobility of the surface chains as temperature is raised, which produces large dynamic loops and makes enzyme degradation possible. The general conclusion is that nigeran single‐crystal surfaces are disordered and increasingly mobile close to their dissolution temperature in water.
Transformation of the ϕ‐ψ plot for proteins to a new representation with local helicity and peptide torsional angles as variables
Authors: Peticolas Warner L. , Kurtz Beth 
Published: December 2004

AbstractA new representation of protein structure is obtained by the angular coordinate transformations ηi = (ϕi+1−ψi)/2 and ξi = ϕi+1+ψi with careful mathematical attention to the cyclical boundary conditions of all of the variables involved. From published ϕ‐ψ data it is possible to obtain a new η‐ξ plot. As the angle ξi is varied from – 180° through 0° to + 180° in this plot, the local helicity of the polypeptide chain changes continuously and contiguously without sudden reversals in handedness. The variable, ηi, gives the torsional position of the ith peptide group. Some peptide groups in proteins, such as the second peptide residue in a type II β‐turn, are nonhydrogen‐bonded and can undergo considerable torsional oscillation. In such cases the η angle should be represented by a line whose length reflects the allowed dynamical variations in the peptide torsional position. Certain peptide residues in proteins may be able to undergo a complete torsional rotation of 360°. Such residues would be represented on the η‐ξ plot as a straight line across the plot parallel to the abscissa. Other examples of the possible usefulness of this plot are also given.
Syn–anti equilibrium of purine bases in dinucleoside monophosphates as studied by proton longitudinal relaxation
Authors: Chachaty Claude , Perly Bruno , Forchioni Alain , Langlet Gérard 
Published: December 2004

AbstractThe preferential orientations of the purine bases in dinucleoside monophosphates such as ApA, ApG, and GpA in 10−2M neutral aqueous solutions have been investigated by proton relaxation at 250 MHz. These orientations are deduced from computer simulations of the magnetization recovery curves following a 180° nonselective pulse. The distances between the H(8) proton of a base and the ribose ring protons which are used in these calculations are obtained by minimization as a function of the glycosyl torsion angle ϒ of the standard deviation between the isotropic reorientation correlation times τR derived from the relaxation rates of these protons. The average H(1′) – H(8) distance obtained by this procedure may be readily verified from the reduction of the H(1′) relaxation rate when H(8) is substituted by a deuteron. The limits of validity of the assumption of a single correlation time τR governing the proton relaxation have been estimated, taking into account several possible internal motions, e.g., the rotation of the base, of the methylene exocyclic group and the N ⇄ S interconversion of the ribose ring. For 10−10 < τR < 2 × 10−10 sec, it appears that the influence of these motions on the proton relaxation becomes perceptible when the jump rates among equilibrium positions exceed ca. 109 sec−1.The whole of the experimental results show that for the ribose ring N conformer, the orientation of the bases is found in the ranges 60° < ϒ < 80° (syn) and 180° < ϒ < 210° (anti). For ribose S conformer, it is observed that this orientation is mainly syn with 5° < ϒ < 90°. The average H(1′) – H(8) distance provides semiquantitative information on the overall syn or anti orientations of the base in each nucleoside moiety. At 298 K the population of the anti conformer is found to increase in the order A‐ pG < Ap‐G ∼ Gp‐A < Ap‐A < A‐pA < G‐pA. A more detailed analysis of relaxation data shows that the maximum possible fraction of the stacked form of dinucleotides, due to the occurrence of N‐anti conformers in both nucleoside moieties, is in the order ApG < GpA < ApA, in agreement with previous works, with however smaller values.Lastly the deuteron linewidth in position 8 of the bases indicates a syn–anti transition rate of the order of 109 sec−1 at room temperature, without noticeable effects therefore on the proton relaxation.
Rigidity of fibrin gels as measured by quasielastic light scattering
Authors: Gelman R. A. , Gladner J. A. , Nossal R. 
Published: December 2004

AbstractThe strength of fibrin gels has been investigated by a recently developed laser light scattering technique for determining the shear modulus of soft gels. By this method, changes in the modulus were monitored as a function of time without perturbing the material. Fibrin gels were crosslinked with blood coagulation factor XIII. Rigidity measurements and SDS–polyacrylamide gel electrophoresis were used to correlate gel strength with the number of covalently bonded subunit chains. The modulus was found to vary linearly with the number of crosslinks until maximum rigidity was achieved.
Physicochemical investigation of k‐carrageenan in the random state
Authors: Vreeman H. J. , Snoeren T. H. M. , Payens T. A. J. 
Published: December 2004

AbstractLight‐scattering, viscosity, and sedimentation experiments on aqueous solutions of k‐carrageenan show that this sulfated polygalactose is an expanded flexible random coil. This expansion is due to long‐range interactions that are predominantly electrostatic. Extrapolation of viscosity data to infinite ionic strength provided values for the intrinsic viscosity which were subjected to the Stockmayer‐Fixman analysis, giving a value for the Mark‐Houwink coefficient under theta‐conditions, Kθ, of 0.27. The characteristic ratio, C∞, under these conditions is 7.8, and the conformation factor σ is 2. In a solution of 0.118 ionic strength, where a Mark‐Houwink exponent aη of 0.86 is found, the radii of gyration calculated from viscosity data are lower than those found from the angular dependence of scattered light. On the other hand, the radius of gyration found from the sedimentation rate agrees well with the light‐scattering radius. The relations between molecular parameters are corrected for the poly‐dispersity of the sample.
Crystal and molecular structure of isoleucinomycin, cyclo[‐(D‐Ile‐Lac‐Ile‐D‐Hyi)3‐](C60H102N6O18)
Authors: Pletnev V. Z. , Galitskii N. M. , Smith G. D. , Weeks C. M. , Duax W. L. 
Published: December 2004

AbstractThe crystal structure of a synthetic analog of valinomycin, cyclo[‐(D‐Ile‐Lac‐Ile‐D‐Hyi)3‐] (C60H102N6O18), has been determined by x‐ray diffraction procedures. The crystals are orthorhombic, space group P212121, with cell parameters a = 11.516, b = 15.705, c = 39.310 Å, and Z = 4. The atomic coordinates for the C, N, O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation. Values of standard (R) and weighted (Rw) reliability factors after refinement are 0.073 and 0.056, respectively. The structure is completely asymmetric. The cyclic molecular backbone is stabilized by six intramolecular hydrogen bonds NH…︁OC, five bonds being of the 4→1 type and one being of the 5→1 type. The side chains are located on the molecular periphery. The conformational state of isoleucinomycin in the crystal is intermediate between the corresponding crystalline states of valinomycin and meso‐valinomycin. The observed conformation suggests that complexation could proceed via entry of the ion at the face possessing the L‐Lac residues, the less crowded face.
Structurally symmetrical, easily polarizable hydrogen bonds between side chains in proteins and proton‐conducting mechanisms. III
Authors: Kristof Wolfgang , Zundel Georg 
Published: December 2004

Abstract(L‐Cys)n, (L‐Lys)n, and (L‐Glu)n were studied by ir spectroscopy in terms of their degree of deprotonation or protonation. It is shown that structurally symmetrical, easily polarizable SH ⃛S− ⇌ −S ⃛HS, N+H ⃛N ⇌ N ⃛H+N, and OH ⃛O− ⇌ −O ⃛HO hydrogen bonds are formed between the side chains. The different wave number distributions of the ir continua caused by these hydrogen bonds show that the barrier in the double‐minimum proton potential decreases in the series of these hydrogen bonds. The stability of these hydrogen bonds against hydration increases in this series. The OH ⃛O− ⇌ −O ⃛HO bonds are not broken by small amounts of water. With (L‐Cys)n the formation of easily polarizable hydrogen bonds and a β‐structure–coil transition are strongly interdependent. As a result of this coupling effect, the β‐structure–coil transition becomes cooperative. With (L‐Glu)n, the formation of the polarizable hydrogen bonds and the observed conformational change are independent processes. The (L‐Glu)n conformation changes from α‐helix to coil only if more than 80% of the residues are deprotonated. Finally, on the basis of the various types of easily polarizable hydrogen bonds, charge shifts in active centers of enzymes and the proton‐conducting mechanism through hydrophobic regions of biological membranes are discussed.
Use of natural‐abundance 15N‐nmr spectroscopy to investigate the secondary structure of peptides: Gramicidin S
Authors: Hawkes Geoffrey E. , Randall Edward W. , Hull William E. , Convert Odile 
Published: December 2004

AbstractThe natural‐abundance 15N‐nuclear magnetic resonance (nmr) spectrum of the cyclic decapeptide gramicidin S has been measured and assigned in the solvents dimethyl sulfoxide, methanol, and 2,2,2‐trifluoroethanol. Three methods have been investigated to distinguish between peptide groups which are exposed to or shielded from the solvent. The solvent dependence of the 15N chemical shift is correlated with the two types of peptide group in gramicidin Sthose with the carbonyl group exposed or shielded from the solvent. The second method monitors the lability of the NH proton (via the collapse of the reduced 15N‐1H coupling) in the presence of added base used to promote intermolecular exchange—peptide protons shielded from the solvent exchange more slowly. The third method looks at the temperature dependence of the 15N chemical shifts in dimethyl sulfoxide. Here the data are not so distinctive as to allow the differentiation between solvent‐exposed or shielded NH bonds at all peptide groups.
Transport properties of oligomeric subunit structures
Authors: Bernal José M. García , De La Torre José García 
Published: December 2004

AbstractThe translational friction coefficients, rotational friction coefficient, and intrinsic viscosity of rigid regular structures composed of up to eight identical spherical subunits have been accurately calculated. The aim of this calculation is to interpret the hydrodynamic properties of oligomeric subunit proteins. To avoid the well‐known failure of the theory in the evaluation of rotational coefficients and intrinsic viscosities, each subunit is hydrodynamically modeled as a polyhedral array of smaller spheres. The analysis of several alternatives suggests that a cubic array is the best choice. The reliability of this strategy is checked by comparison of the calculated values for all the transport properties of a sphere and the translational friction coefficients of a dimer with their exact values. Finally, the hydrodynamic properties of a number of subunit structures with varying number of subunits and different geometries are tabulated.
Physical properties of type i collagen in solution: Structure of α‐Chains and β‐ and γ‐components and two‐component mixtures
Authors: Silver F. H. , Trelstad R. L. 
Published: December 2004

AbstractThe structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α‐chains and β‐ and γ‐components are 1.550 ± 0.08 × 10−7, 1.000 ± 0.05 × 10−7, and 0.835 ± 0.04 × 10−7 cm2/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α‐chain), 21.5 nm (β‐component), and 25.7 nm (γ‐component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α‐chains and β‐and γ‐components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.
Spectroscopic investigations of peptide 401 from bee venom
Authors: Walde P. , Jäckle H. , Luisi P. L. , Dempsey C. J. , Banks B. E. C. 
Published: December 2004

AbstractThe circular dichroism (CD) and 1H‐nmr properties of peptide 401, a bee venom component with 22 amino acid residues and two disulfide bridges, have been studied under a variety of conditions and compared with those of the structurally related octadecapeptide apamin. The major component of the relatively intense CD signal in the 200–230‐nm region in both cases probably arises from the rigid asymmetric ring structures of the disulfide bridges. CD spectra are practically unaffected by pH (in the region 1–7), solvent (water, trifluoroethanol, dioxane/water mixtures), concentration of peptide, or additions of salt (guanidinium chloride, KCl). Temperature changes (in the range 20–59°C) have only a modest influence. For both apamin and peptide 401, reduction of the two disulfide bridges results in a dramatic change of the CD spectrum, which acquires the characteristic form of a random coil. Preliminary 1H‐nmr data are presented for both the reduced and the oxidized form. Several resonance peaks could be assigned on the basis of the theoretical random‐coil spectrum. In the oxidized forms, six slowly exchangeable amide protons could be found in a spectrum taken at low pH, which are ascribed to intramolecular hydrogen bonds. Each of the four protons of the two histidine residues of peptide 401 appears as two distinct resonance peaks in the oxidized form but not in the reduced form. This is interpreted as arising from conformational heterogeneity of peptide 401.
Simulations of the solvent structure for macromolecules. I. Solvation of B‐DNA double helix at T = 300 K
Authors: Corongiu Giorgina , Clementi Enrico 
Published: December 2004

AbstractMonte Carlo simulations are reported for a system of 447 water molecules enclosing a B‐DNA double‐helix fragment with 12 base pairs and the corresponding sugar and phosphate units. From a detailed analysis on the interaction energies and probability distributions (at a simulated temperature of 300 K), the water molecules can be partitioned into clusters strongly interacting with (1) the phosphates, (2) the sugars, (3) the sugars and the bases, and (4) the base pairs. In addition, transgroove and interphosphate filament of hydrogen‐bonded water molecules have been detected. From simulations performed with variable numbers of water molecules, a theoretical isotherm has been obtained, with the characteristic sigmoidal shape, known from absorption–desorption experiments on related systems. The expected main features for the structure of water molecules solvating B‐DNA with Na+ counterions are briefly discussed at the end of the paper.
Physicochemical parameters of partially hydrolyzed S. salivarius levan fractions
Authors: Stivala S. S. , Zweig J. E. 
Published: December 2004

AbstractThe fractions obtained from the partially hydrolyzed branched Streptococcus salivarius levan were examined in solution. Sedimentation coefficients, S0, intrinsic viscosities, [η], weight‐average molecular weights, Mw, and radii of gyration were obtained from sedimentation velocity, viscosity, and light‐scattering measurements. Double logarithmic plots of [η] vs Mw and S0 vs Mw each yielded two linear segments intersecting at Mw ≈ 105. Hydrodynamic data suggest that fractions of Mw > 105 behave as compact spheres, whereas for Mw < 105, the particles are best characterized as linear random coils. Calculations based on theories of random coils and spheres support the above observations.
Stability and geometry of hydrogen‐bonded complexes of peptides
Authors: Madison Vincent , Lasky Jerry , Currie Bruce 
Published: December 2004

AbstractObservations of induced circular dichroism (CD) bands in chloroform solution demonstrate the formation of specific, asymmetric complexes of the aromatic ligands 2‐pyridone and 2,6‐dichlorobenzoic acid with cyclic dipeptides of the general formula cyclo(L‐Pro‐X). The induced CD changes sign with the configuration of X due to subtle influences of the side chain on the geometry of the complex. Computations of interaction energies suggest that a plausible model for the complex of an aromatic ligand with the ‐CONH‐ of the cis secondary amide is a nearly planar arrangement of six heavy atoms in a ring containing two hydrogen bonds. The observed CD is matched by that computed for a tilt of the aromatic ligand toward the side chain of X. Binding constants were determined from the induced CD as a function of ligand concentration. For dichlorobenzoic acid these are about 450m−1 for the secondary amide and 50m−1 for the tertiary amide. For pyridone the binding constant is about 45m−1 for either the secondary or tertiary amide. For comparison self‐dimerization constants determined by vapor‐pressure osmometry in chloroform solution at 25°C are 870, 350, 50, and 20m−1 for pyridone, benzoic acid, dichlorobenzoic acid, and cyclo(L‐Pro‐Gly), respectively.