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PubMedDate not supplied

[Molecular morphology of eukaryotic class I translation termination factor eRF1 in solution].

The integral structural parameters and the shape of the molecule of human translation termination factor eRF1 were determined from the small-angle X-ray scattering in solution. The molecular shapes were found by bead modeling with nonlinear minimization of the root-mean-square deviation of the calculated from the experimental scattering curve. Comparisons of the small-angle scattering curves computed for atomic-resolution structures of eRF1 with the experimental data on scattering from solution testified that the crystal and the solution conformations are close. In the ribosome, the distance between the eRF1 motifs GGQ and NIKS must be shorter than in crystal or solution (75 versus 107-112 A). Therefore, like its bacterial counterpart RF2, the eukaryotic eRF1 must change its conformation as it binds to the ribosome. The conformational mobility of eukaryotic and prokaryotic class-1 release factors is another feature making them functionally akin to tRNA.

DNA-Binding Proteins↗

PubMed1978

Study of DNA-spermine interactions by use of small-angle and wide-angle X-ray scattering and circular dichroism.

Circular dichroism measurements with DNA-spermine complexes at 0.075 M NaCl and at 0.15 M NaCl reveal +psi (type I) and -psi (type II) CD spectra respectively. From small-angle X-ray scattering studies it could be shown that type I has a long-range order, short-range order supramolecular structure, while type II is of long-range disorder, short-range disorder structure. The secondary structure of the DNA in both types of condensates is B-like as concluded from wide-angle X-ray scattering diagrams of the condensates and from a comparison with the wide-angle X-ray curves of DNA and RNA in solution.

Animals↗

PubMed1979

Multiangle light scattering flow photometry of cultured human fibroblasts: comparison of normal cells with a mutant line containing cytoplasmic inclusions.

Multi-angle light scattering flow photometry was used to study the light scattering properties of normal cultured fibroblasts and a mutant fibroblast line containing cytoplasmic lysosomal inclusions. The effect of glutaraldehyde fixation on the light scattering properties of the cells was also examined and correlated with their ultrastructure. Normal fibroblasts showed uniform organelle distribution with few vacuoles or dense bodies in the cytoplasm while the mutant line showed abnormal cytoplasmic inclusions of varying morphology, density and lucency. As predicted by light scattering theory, the mutant cells containing the cytoplasmic inclusions scattered more light at large angles (greater than theta = 1.85 degrees) than did the normal cells. Glutaraldehyde fixation decreased light scattering at small angles (less than theta = 1.85 degrees), increased light scattering at larger angles (greater than theta = 1.85 degrees) in both normal and mutant cells and enhanced resolution of the light scattering signatures. The mutant line scattered 2-3 times more light at a wide angle (greater than theta = 12.74 degrees) than did the normal cells. These data suggest that abnormal lysosomal storage inclusion bodies in the cytoplasm of the cells can be detected by differential light scattering methods.

Cell Line↗

PubMed1961

The structure of high molecular weight ribonucleic acid in solution. A smallangle x-ray scattering study.

Small-angle x-ray scattering studies on an absolute scale have been carried out on isotropic solutions of high molecular weight RNA obtained from ascites tumor cells, E. coli, and yeast. It was found that in all three cases the RNA is composed of short rigid rods (50 to 150A in length) joined by small flexible regions. The rods account for almost the entire structure (at least 90 per cent); their radius of gyration about the axis and their mass per unit length are similar to those of DNA, suggesting a double-stranded helical structure. The rods are joined in an array forming the compact RNA molecule. On thermal degradation, the molecular superstructure disappears while the rods persist.

Escherichia coli↗

PubMed2005

Neutron scattering from equilibrium-swollen networks.

Small-angle neutron scattering measurements were performed on end-linked poly (dimethylsiloxane) (PDMS) networks swollen to equilibrium with d-benzene. Comparison was made with equivalent concentration PDMS solutions. Equilibrium-swollen networks consistently displayed a linear scattering regime at low q followed by a good-solvent-like scaling regime at high q in agreement with the predictions of the Gel Tensile Blob (GTB) model. Data are fit using the unified function modified for the GTB model (3-parameter fit). Equilibrium-swollen networks display a base structural size, the gel tensile-blob size, xi, that was found to be independent of the molecular weight between crosslinks for the series of molecular weights studied, consistent with the predictions of the model. The length of the extended tensile structure, L, can be larger than the length of the fully extended network strand. The predicted scaling relationship for L, L approximately Q(1/2)N(avg), where N(avg) = (1/fN(c)(2) + 1/4N(e)(2), Q is the equilibrium swelling ratio, N(c) is the molecular weight between crosslinks, N(e) is the entanglement molecular weight and f is the crosslink functionality is in agreement with experimental results for the networks studied.

Journal Article↗

PubMed2006

ASAXS, SAXS and SANS investigations of vulcanized elastomers filled with carbon black.

Small-angle X-ray scattering (SAXS) performed down to small q values (q <or= 10(-3) A(-1)) is a powerful method for investigating the arrangement of filler aggregates in filled elastomers under uniaxial strain. Meanwhile, for vulcanized samples, zinc oxide is used as an additive. Owing to their high contrast, the ZnO particles remaining in the manufactured composite are strong X-ray scatterers. In the low-q domain, their scattering hides that of filler aggregates (carbon black, pyrogenic silica) and must be quantified in order to be suppressed. To this end, anomalous SAXS (ASAXS) and small-angle neutron scattering (SANS) have been performed. It is shown that ASAXS measurements can be performed down to small q values (q <or= 10(-3) A(-1)). Therefore ASAXS is well adapted to separate the contributions of ZnO and filler scattering. For neutron scattering the contrast of the ZnO particles is similar to that of carbon. Because the amount of ZnO is much smaller than that of filler, ZnO scattering can be neglected. Owing to multiple scattering effects, however, SANS can only be used for very thin samples (less than about 0.25 mm). It is shown that, providing multiple scattering is avoided, ASAXS and SANS yield similar scattering curves for the filler aggregates.

Elastomers↗

PubMed1999

Differences between the pressure- and temperature-induced denaturation and aggregation of beta-lactoglobulin A, B, and AB monitored by FT-IR spectroscopy and small-angle X-ray scattering.

We examined the temperature- and pressure-induced unfolding and aggregation of beta-lactoglobulin (beta-Lg) and its genetic variants A and B up to temperatures of 90 degrees C in the pressure range from 1 bar to 10 kbar. To achieve information simultaneously on the secondary, tertiary, and quaternary structures, we have applied Synchrotron small-angle X-ray diffraction and Fourier transform infrared spectroscopy. Upon heating a beta-Lg solution at pH 7.0, the radius of gyration Rg first decreases, indicating a partial dissociation of the dimer into the monomers, the secondary structures remaining essentially unchanged. Above 50 degrees C, the infrared spectroscopy data reveal a decrease in intramolecular beta-sheet and alpha-helical structures, whereas the contribution of disordered structures increases. Within the temperature range from 50 to 60 degrees C, the appearance of the pair distance distribution function is not altered significantly, whereas the amount of defined secondary structures declines approximately by 10%. Above 60 degrees C the aggregation process of 1% beta-Lg solutions is clearly detectable by the increase in Rg and intermolecular beta-sheet content. The irreversible aggregation is due to intermolecular S-H/S-S interchange reactions and hydrophobic interactions. Upon pressurization at room temperature, the equilibrium between monomers and dimers is also shifted and dissociation of dimers is induced. At pressures of approximately 1300 bar, the amount of beta-sheet and alpha-helical structures decreases and the content of disordered structures increases, indicating the beginning unfolding of the protein which enables aggregation. Contrary to the thermal denaturation process, intermolecular beta-sheet formation is of less importance in pressure-induced protein aggregation and gelation. The spatial extent of the resulting protein clusters is time- and concentration-dependent. The aggregation of a 1% (w/w) solution of A, B, and the mixture AB results in the formation of at least octameric units as can be deduced from the radius of gyration of about 36 A. No differences in the pressure stability of the different genetic variants of beta-Lg are detectable in our FT-IR and SAXS experiments. Even application of higher pressures (up to 10 kbar) does not result in complete unfolding of all beta-Lg variants.

Amino Acid Substitution↗

PubMed2004

Structure of conditioned sludge flocs.

Free settling tests, small-angle light scattering, microtome-slicing techniques, and confocal laser scanning microscopy were performed to examine how the cationic flocculation or freezing and thawing affected the floc structure. The floc size, internal pore size, mass fractal dimensions determined from free-settling test or small angle light scattering test, aeral porosity, boundary fractal dimension and Sierpinski carpet fractal dimension of pore boundary from 2D slices, and the volume porosity, compactness, and the pores' box-counting fractal dimension from 3D reconstructed image, were estimated and compared. Cationic flocculation would produce large flocs with internal pores of shape resembling a long "tube" with rough surface. Freezing and thawing would produce flocs with internal pores with lower aspect ratio and a smoother boundary.

Bacteria↗

PubMedDate not supplied

The collagen fibers of the anteroinferior capsulolabrum have multiaxial orientation to resist shoulder dislocation.

Instability of the glenohumeral joint can be associated with anteroinferior capsulolabral rupture. To understand its static stabilizing effect better, the collagen fiber orientation of the inferior glenohumeral ligament (IGHL), a component of the anteroinferior capsulolabrum, was studied with a small angle light scattering technique. Three rectangular samples (approximately 11 x 6 mm) were excised from the axillary pouch, one from the anterior band (AB) of the IGHL and one control sample from the long head of the biceps tendon of 7 cadaveric shoulders. The small angle light scattering technique scans the tissue with a helium-neon laser beam and quantifies the fiber alignment based on the resultant scattering pattern. The fiber orientation was quantified by an orientation index, defined as the angle within which 50% of the fibers lie. The axillary pouch had a random orientation, whereas the AB-IGHL was random with some regions of localized alignment. The percentage of tissue with an orientation index range of 25 degrees to 45 degrees was 23.2% +/- 8.5% and 29.0% +/- 13.1% for the axillary pouch and the AB-IGHL, respectively, whereas that for the long head of the biceps tendon was 61.6% +/- 15.2%. This suggests that the collagen fibers in the IGHL are not highly aligned and the anteroinferior capsulolabrum can be modeled as a continuous sheet. Moreover, a biomechanical evaluation of the anteroinferior capsulolabrum that investigates the possibility that the mechanical properties may be directionally independent should be conducted.

Adult↗

PubMed1984

[A new particle of chromatin obtained by proteolysis of histones with clostripain].

The proteolysis of the chromatin core particle by the arginine-specific endopeptidase clostripain yields a new nucleoprotein particle containing an unaltered DNA fragment of about 145 base pairs in length and a protein octameric core made up of twice the four histone fragments H2A, H2B, H3 and H4. This composition is suggested by the molecular weight of about 180 kd determined for the new particle by small angle neutron scattering. The histone fragments differ by about 2-3 kd each from the initial histones H2A, H2B, H3 and H4 and they correspond to the cleavage of the N-terminal part of the sequence (20-30 residues). A preliminary investigation by thermal denaturation, circular dichroism and small angle neutron scattering (measurement of a radius of gyration by the H2O-D2O contrast variation technique) indicates that the spatial organization of the new chromatin particle closely resembles that of the initial core particle.

Chemical Phenomena↗

PubMed1994

Study of nucleation-related phenomena in lysozyme solutions. Application to gel growth.

Two populations of aggregates are generally indentified in supersaturated solutions of biological macromolecules: small aggregates of a size which is less than 5 nm and large aggregates, the largest of which are at least one order of magnitude bigger. In order to understand the role played by the microporous network of a gel in the growth and behaviour of these different species in the prenucleation period, an in situ observation of nucleation has been carried out using either free solutions or solutions trapped in agarose gels. In a previous study, free solutions were investigated by small-angle neutron scattering (SANS) to identify the small aggregates. Optical observations, made under the same conditions, revealed the formation of an amorphous precipitate which disappeared at the end of the experiment. The sedimentation of this phase, which occurs in free solution but never occurs in gelled solution, depletes the solution bulk and this could explain why the nucleation density is higher in agarose gel than in free solution. The case of silica gel, the behaviour of which is completely different with respect to nucleation, will be discussed.

Journal Article↗

PubMed1989

The location of DNA in complexes of recA protein with double-stranded DNA. A neutron scattering study.

Purified recA protein is found as rodlike homopolymers, and it forms filamentous complexes with double-stranded DNA that are stable in the presence of ATP gamma S, a nonhydrolyzable analogue of ATP. The structure of these filaments has been described in some detail by electron microscopy. Here we confirm the mass per length of 6.5 recA/100 A in solution by small-angle neutron scattering and extend the analysis to homopolymers of recA protein, finding a mass per length of about 7 recA/100 A and a radial mass distribution (cross-sectional radius of gyration) significantly different for the two filaments. The models proposed so far for the structure of the complex have placed the DNA in the center of the filament. Here we verify this assumption using small-angle neutron scattering to locate the DNA in the complexes, exploiting the contrast variation method in D2O/H2O mixtures. Model calculations show that the natural contrast difference between DNA and protein is not sufficient to locate the DNA (which accounts for only 4.7% of the mass in the complex). When deuterated DNA is used, the contrast difference is enhanced, and model calculations and experiment then converge, indicating that the DNA is indeed near the axis of the complex.

Binding Sites↗

PubMed2002

Structural insights into the beta-mannosidase from T. reesei obtained by synchrotron small-angle X-ray solution scattering enhanced by X-ray crystallography.

A molecular envelope of the beta-mannosidase from Trichoderma reesei has been obtained by combined use of solution small-angle X-ray scattering (SAXS) and protein crystallography. Crystallographic data at 4 A resolution have been used to enhance informational content of the SAXS data and to obtain an independent, more detailed protein shape. The phased molecular replacement technique using a low resolution SAXS model, building, and refinement of a free atom model has been employed successfully. The SAXS and crystallographic free atom models exhibit a similar globular form and were used to assess available crystallographic models of glycosyl hydrolases. The structure of the beta-galactosidase, a member of a family 2, clan GHA glycosyl hydrolases, shows an excellent fit to the experimental molecular envelope and distance distribution function of the beta-mannosidase, indicating gross similarities in their three-dimensional structures. The secondary structure of beta-mannosidase quantified by circular dichroism measurements is in a good agreement with that of beta-galactosidase. We show that a comparison of distance distribution functions in combination with 1D and 2D sequence alignment techniques was able to restrict the number of possible structurally homologous proteins. The method could be applied as a general method in structural genomics and related fields once protein solution scattering data are available.

Circular Dichroism↗

PubMed2003

Effect of multiple scattering on SANS spectra from bicontinuous microemulsions.

Small-angle neutron scattering is a powerful tool for investigating the microstructure of self-assembled systems. The domain length, d, and the correlation length, xi, are two measures of bicontinuous microemulsions that are often determined from coherent SANS spectra. Some microemulsions scatter strongly, however, so measured spectra can contain multiple coherent scattering, and neglect of that multiple scattering can lead to incorrect values of d and xi. In addition, multiple scattering can give rise to artifacts in the spectra, most notably an apparent scattering peak at twice the value of the scattering vector of the main peak. Here, changes in the SANS spectra from strongly scattering microemulsions and the parameters derived from them are reported as a function of relative scattering probability by varying both sample thickness and scattering contrast. A linear extrapolation of the results to zero scattering probability yields good estimates for the microstructural parameters, and the numerical procedure of Schelten and Schmatz is used to calculate the specific effects of multiple scattering on typical bicontinuous microemulsion scattering spectra.

Journal Article↗

PubMed2006

Influence of pressure on structure and dynamics of bovine pancreatic trypsin inhibitor (BPTI): small angle and quasi-elastic neutron scattering studies.

We have studied the influence of pressure on structure and dynamics of a small protein belonging to the enzymatic catalysis: the bovine pancreatic trypsin inhibitor (BPTI). Using a copper-beryllium high-pressure cell, we have performed small angle neutron scattering (SANS) experiment on NEAT spectrometer at HMI (Berlin, Germany). In the SANS configuration, the evolution of the radius of gyration and of the shape of the protein under pressures up to 6,000 bar has been studied. When increasing pressure from atmospheric pressure up to 6,000 bar, the pressure effects on the global structure of BPTI result on a reduction of the radius of gyration from 13.4 A down to 12.0 A. Between 5,000 and 6,000 bar, some transition already detected by FTIR [N. Takeda, K. Nakano, M. Kato, Y. Taniguchi, Biospectroscopy, 4, 1998, pp. 209-216] is observed. The pressure effect is not reversible because the initial value of the radius of gyration is not recovered after pressure release. By extending the range of wave-vectors to high q, we have observed a change of the form factor (shape) of the BPTI under pressure. At atmospheric pressure BPTI exhibits an ellipsoidal form factor that is characteristic of the native state. When the pressure is increased from atmospheric pressure up to 6,000 bar, the protein keeps its ellipsoidal shape. The parameters of the ellipsoid vary and the transition detected between 5,000 and 6,000 bar in the form factor of BPTI is in agreement with the FTIR results. After pressure release, the form factor of BPTI is characteristic of an ellipsoid of revolution with a semi-axis a, slightly elongated with respect to that of the native one, indicating that the pressure-induced structural changes on the protein are not reversible. The global motions and the internal dynamics of BPTI protein have been investigated in the same pressure range by quasi-elastic neutron scattering experiments on IN5 time-of-flight spectrometer at ILL (Grenoble, France). The diffusion coefficients D and the internal relaxation times of BPTI deduced from the analysis of the intermediate scattering functions show a slowing down of protein dynamics when increasing pressure.

Animals↗

PubMed1978

[Secondary structure of condensed DNA. wide-angle, small-angle x-ray scattering and circular dichroism].

Ethanol precipitated DNA shows a CD spectrum of the +psi-type which is similar to that of DNA in the A-form. DNA condensed with cetyl-trimethylammonium-bromide shows, depending on the condensation velocity, a CD spectrum of the -psi-type, or a CD spectrum only slightly modified from that of DNA in solution. The first spectrum is similar to that of DNA in the C-form, and the second one, to that of DNA in the B-form. Using large-angle X-ray scattering of the three DNA condensates and comparing them with the scattering curves calculated from the atom coordinates for the A-, B-, and C-form of DNA it is shown that the secondary structure of the DNA belongs in all three cases to the B-family. It follows from this result that the secondary structure of DNA alone does not determine the type of CD spectrum. The CD spectrum of condensed DNA is essentially determined by the supramolecular structures of the partially crystalline DNA condensates. These supramolecular structures can be demonstrated by the small-angle X-ray diagrams. The condensation of DNA by ethanol and cetyl-trimethylammonium-bromide proceeds in the form of a partial crystallization of the DNA.

Animals↗

PubMed1983

Anomalous x-ray scattering from terbium-labeled parvalbumin in solution.

We have used anomalous small-angle x-ray scattering as a structural probe for solutions of rabbit parvalbumin labeled with terbium. This technique makes use of the large changes in the terbium scattering factor that occur when the x-ray energy is tuned around an L3 absorption edge of this heavy-atom label. These changes in scattering result in changes in the small-angle scattering curve of the labeled protein as a whole, which can then be analyzed to derive structural information concerning the distribution of labels in the protein. Based on a Gaussian model for the protein electron density, the mean distance from the terbiums to the protein center of mass is determined to be 13.2 A and is consistent with crystallographic results. Our results demonstrate the usefulness of terbium as an anomalous scattering label and provide criteria to help establish anomalous scattering as a reliable structural technique for proteins in solution.

Animals↗

PubMed1998

A core-shell model of calcium phosphate nanoclusters stabilized by beta-casein phosphopeptides, derived from sedimentation equilibrium and small-angle X-ray and neutron-scattering measurements.

Calcium phosphate nanoclusters were prepared under standardised conditions using 10 mg ml(-1) of the 25-amino-acid N-terminal tryptic phosphopeptide of bovine beta-casein as a stabilising agent. The Mr determined by sedimentation equilibrium was 197,600+/-13,700 and the apparent radius of gyration determined by X-ray scattering was 2.80+/-0.05 nm. A small-angle neutron scattering contrast variation study in 1H2O/2H2O mixtures was performed and gave radii of gyration at the calculated match points for the calcium phosphate (88.2% 2H2O) and phosphopeptide (41.3% 2H2O) of 3.39+/-0.08 nm and 1.85+/-0.05 nm, respectively. Measurements at larger scattering wave vector showed a subsidiary maximum at about Q = 1.6 nm(-1). The results are consistent with a model of the nanoclusters comprising a spherical core of 355+/-20 CaHPO4 x 2 H2O units, density 2.31 g ml(-1) and radius 2.30+/-0.05 nm surrounded by 49+/-4 peptide chains with a partial specific volume of 0.7 cm3 g(-1), forming a tightly packed shell with an outer radius of 4.04+/-0.15 nm. This model suggests that the phosphopeptide is able to arrest the process of growth of the precipitating phase of calcium phosphate at its earliest stages. A similar role for whole casein could be vital to the normal functioning of the mammary gland during milk secretion.

Calcium Phosphates↗