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Results for “Scattering, Small Angle”

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PubMed2006

A small-angle X-ray scattering study of the interactions in concentrated silica colloidal dispersions.

The structure factors of colloidal silica dispersions at rather high volume fractions (from 0.055 to 0.22) were measured by small-angle X-ray scattering and fitted with both the equivalent hard-sphere potential model (EHS) and the Hayter-Penfold/Yukawa potential model (HPY). Both of these models described the interactions in these dispersions successfully, and the results were in reasonable agreement. The strength and range of the interaction potentials decreased with increasing particle volume fractions, which suggests shrinkage of the electrical double layer arising from an increase in the counterion concentration in the bulk solution. However, the interactions at the average interparticle separation increased as the volume fraction increased. The interaction ranges (delta) determined by the two models were very similar. Structure factors were also used to determine the size and volume fraction of the particles. The values of the size obtained from the structure factors were slightly larger than those obtained from the form factors; this difference is ascribed to the nonspherical shape and polydispersity of the colloidal particles. The volume fractions measured by these two methods were very similar and are both in good agreement with the independently measured results.

Journal Article↗

PubMed1982

Structural variability of tRNA: small-angle x-ray scattering of the yeast tRNAphe-Escherichia coli tRNAGlu2 complex.

The structure of the complex formed in solution between yeast tRNAPhe and Escherichia coli tRNAGlu2 has been studied by small-angle x-ray scattering. The complex has a radius of gyration of 4.0 nm and an electron-pair distance distribution that is incompatible with a model composed to two tRNAs joined at their complementary anticodons and exhibiting the L shape seen in the crystal. Instead a model in which the two tRNAs, still bound via the anticodons, assume a conformation with the acceptor arms folded toward the anticodon arms agrees with the observed scattering curves.

Anticodon↗

PubMed1985

Conformation of human IgG subclasses in solution. Small-angle X-ray scattering and hydrodynamic studies.

The structure of six human myeloma proteins: IgG1(Bal), IgG2(Klu), IgG3(Bak), IgG3(Het), IgG4(Kov) and IgG4(Pol), was studied in solution using small-angle X-ray scattering and hydrodynamic methods. For IgG1(Bal) and IgG3(Het) the experimental data, including radius of gyration (Rg degree), radii of gyration of the cross-section (Rq1, Rq2), intrinsic viscosity [eta], sedimentation coefficient (S degree 20,w) and molecular mass, were interpreted in terms of structural models based on the Fab and Fc conformations, observed in crystal, by varying the relative positions of the Fab and Fc parts, i.e. their relative angles and distances. The values Rg degree = (6.00 +/- 0.05) nm, S degree 20,w = (6.81 +/- 0.10) S and [eta] = 0.0062 +/- 0.0005 cm3/mg obtained for IgG1(Bal) are compatible with a planar model in which the angle between the Fab arms is about 120 degrees. For IgG3(Het) the following data were obtained: Rg degree = (4.90 +/- 0.05) nm, S degree 20,w = (6.32 +/- 0.01) S and [eta] = (0.0065 +/- 0.0005) cm3/mg. The apparent contradiction between the higher molecular mass and lower Rg degree and S degree 20,w values for IgG3(Het) in comparison to IgG1(Bal) can be resolved by proposing a 'non-planar' (tetrahedral) molecular shape, in which the long hinge peptide is in a folded conformation and the two Fab and Fc parts are in a closely packed arrangement. In this model the angle between the two Fab arms is about 90 degrees, in the average position. The X-ray scattering and hydrodynamic behaviour of the IgG2 and IgG4 types of antibodies appeared to be similar to IgG1(Bal). The parameters of the two IgG3 proteins are similar while they are different to the others.

Amino Acids↗

PubMedDate not supplied

Small-angle X-ray scattering studies on the X-ray aggregation of malate synthase. Computer simulations and models.

Malate synthase undergoes an X-ray induced aggregation which can be monitored in situ by small-angle X-ray scattering; the analysis of scattering curves, taken at subsequent stages of aggregation, has led to the establishment of a tentative model for an aggregation in two dimensions (Zipper and Durchschlag (1980) Rad. and Environm. Biophys., in press). This model was checked by comparison of appropriate theoretical curves with the experimental curves. The theoretical scattering curves for this comparison were obtained by weighted averaging over the scattering curves calculated for various species of hypothetical aggregates. Based on the approximation of the unaggregated enzyme particle by an oblate cylinder, the aggregates were assumed to be composed of 2, 3, 4 or 6 of such cylinders, associated side-by-side in one and later on in two linear rows. THe weight fractions of the species were chosen so, that an optimum fit of the experimental mean radii of gyration and mean degrees of aggregation was achieved. The distance distribution functions calculated for the model are very similar to the functions derived from the scattering experiment. Cross-section Guinier plots of the scattering curves of the model reveal the occurrence of one and later on of two pseudo cross-section factors similar to those observed in the experimental scattering curves. The pseudo thickness factor of the model of the unaggregated particle is found to be retained in the model curves for all stages of aggregation. From these results it can be concluded that the model for the aggregation process is essentially consistent with the scattering behaviour of the aggregating enzyme. Small differences between the theoretical and experimental curves may be explained by the idealizations of the model. The comparison of theoretical curves for alternative models, assuming aggregation in three dimensions, suggests that these models are unlikely, though small amounts of three-dimensional aggregates cannot be ruled out completely.

Computers↗

PubMed1996

Characterization of bone mineral crystals in horse radius by small-angle X-ray scattering.

The size and the orientation of the bone salt (mineral) crystals in the cranial and caudal zones in the transverse midshaft section of the equine radius were investigated by small-angle X-ray scattering (SAXS). The results are interpreted as indicating that the crystals had an elongated shape with an average thickness of T = 3.17 +/- 0. 15 nm in the caudal region and T = 3.79 +/- 0.20 nm in the cranial region. Their orientation was predominantly in the longitudinal direction of the bone. There was no preferential orientation within the transverse plane. The distribution of tilt angles with respect to the longitudinal direction was determined directly from the SAXS data: the average angle was about 30 degrees for the cranial region and 45 degrees for the caudal region. Assuming that the needle-like crystals are parallel with the collagen fibrils, the angular distribution of the crystals is in good agreement with previous measurements of collagen orientation using circularly polarized light microscopy.

Animals↗

PubMed1997

Structural analysis of A-protein of cucumber green mottle mosaic virus and tobacco mosaic virus by synchrotron small-angle X-ray scattering.

The size and shape of A-protein of tobacco mosaic virus coat protein (TMVP) and cucumber green mottle mosaic virus coat protein (CGMMVP) were evaluated by means of small-angle X-ray scattering (SAXS) using a synchrotron radiation source, complemented by electron microscopic observations. The results imply that TMV and CGMMV A-proteins are composed of three and two subunits, respectively, stacked in the shape of an isosceles triangular prism at lower ionic strength. Considering the difference of the A-protein structure at higher and lower ionic strength, the globular core structure was proposed as a subunit which might be modeled as a thin isosceles triangular prism composed of four globular cores joined by rather flexible segments. These cores correspond probably to four helical regions in a subunit, and rearrange their relative positions according to the external conditions. A slight rearrangement of core positions in a subunit may result in the formation of A-proteins of various shapes.

Capsid↗

PubMed2001

Time resolved collapse of a folding protein observed with small angle x-ray scattering.

High-intensity, "pink" beam from an undulator was used in conjunction with microfabricated rapid-fluid mixing devices to monitor the early events in protein folding with time resolved small angle x-ray scattering. This Letter describes recent work on the protein bovine beta-lactoglobulin where collapse from an expanded to a compact set of states was directly observed on the millisecond time scale. The role of chain collapse, one of the initial stages of protein folding, is not currently understood. The characterization of transient, compact states is vital in assessing the validity of theories and models of the folding process.

Animals↗

PubMed1992

Small-angle x-ray scattering study of metal ion-induced conformational changes in Serratia protease.

Metal ion-induced conformational changes in Serratia protease which contains one zinc ion per molecule were investigated by the small-angle x-ray scattering method. The molecule is an elongated ellipsoid of approximately 110 x 40 x 40 A with a large cleft in its central region. Comparisons of the native (zinc-enzyme) with the zinc-free (apoenzyme) enzyme and with the zinc-replated metalloenzyme show small but significant differences in their radii of gyration, maximum particle dimensions, and intraparticle pair-distance distributions. The radius of gyration and maximum particle dimension of the native enzyme are almost the same as those of the cobalt-enzyme but are shorter and longer, respectively, than those of the apo- and cadmium-enzymes. Simulation analysis based on the intraparticle pair-distribution function showed that these modified enzymes are comparable with the native enzyme in overall structure, and, except for the cobalt-enzyme, differ in cleft size. The residual enzymatic activity of the cobalt-enzyme is the same as that of the native enzyme, but the apo- and cadmium-enzymes have considerably less activity. The size of the cleft therefore is strictly controlled to ensure optimal enzyme activity, and the position and coordination behavior of the zinc ion in the cleft appears to be essential both for biological functioning and for the maintenance of the gross tertiary structure.

Metalloendopeptidases↗

PubMed2004

Structure and dynamics of the nucleocapsid-binding domain of the Sendai virus phosphoprotein in solution.

The RNA-dependent RNA polymerase of the Sendai virus (SeV) consists of the large protein (L) and the phosphoprotein (P). P plays a crucial role in the enzyme by positioning L (which carries the polymerase activity) onto the matrix for transcription and replication formed by the RNA and the nucleoprotein, the N-RNA. P has a modular structure with distinct functional domains: an N-terminal domain involved in binding to N degrees (N that is not yet bound to RNA) and a C-terminal domain that carries the oligomerisation domain, the N-RNA binding domain and the L binding domain and that, combined with L, is active in transcription. Structural data have previously been obtained on the N-terminal domain and on the oligomerisation domain of P, but not yet on its N-RNA binding domain (also-called the X protein). Here we present an NMR and a small angle neutron scattering study of the SeV X protein. We show that this molecule presents two subdomains linked by an 11-residue linker, with the N-subdomain lacking a well-defined conformation. The 3D structure of the C-subdomain consists of three alpha-helices revealing an asymmetric charge distribution that may be important for binding to RNA-bound nucleoprotein. The structure of the entire C-terminal domain of P is modelled from its constituent parts in combination with small angle scattering data on this domain.

Amino Acid Sequence↗

PubMed2005

In situ investigations on organic foam films using neutron and synchrotron radiation.

We report on small-angle neutron scattering (SANS) and X-ray scattering (SAXS) investigations of foam films stabilized by sodium dodecyl sulfate. Previous measurements on dry foams (Axelos, M. A. V.; Boue, B. Langmuir 2003, 19, 6598) have shown the presence of spikes in the two-dimensional scattering data which suggest that the incident beam is reflected on some film surfaces. The latter interpretation is confirmed by new neutron studies performed on ordered ("bamboo") foams which allow selection of single films. In the first case, we show that the spikes of the scattered intensity can be obtained by reflection on two parts of the foam, namely, the films and the Plateau borders. With synchrotron radiation, first observations of distinct interference fringes have allowed an accurate determination of the film thickness. A comparison with X-ray and neutron data is made, opening a general discussion about the capabilities of small-angle scattering techniques for studying the microscopic properties of foam films.

Journal Article↗

PubMed1997

Small-Angle X-Ray Scattering Study of the Formation of Colloidal Silica Particles from Alkoxides: Primary Particles or Not?

The formation of colloidal silica particles and the dynamics of the nanostructure of the particles are investigated by small-angle X-ray scattering (SAXS) technique. Solute concentrations of 0.5 M tetraethylorthosilicate (TEOS), 1.1 or 2.2 M water (H2O), and 0.04 or 0.1 M ammonia base (NH3) in ethanol were used to obtain reaction conditions as close to those of the Stober method as possible and to have reaction kinetics that were slow enough to probe the changes in the nanostructure of the growing particles and to obtain good statistics from the SAXS measurements. We measured the changes in the radius of gyration and the fractal dimension as a function of time during growth. Remarkably, we find that, after an induction period, the first particles to appear in the solution have a radius of gyration of approximately 10 nm and are mass fractals characterized by their polymeric, open structure. This stage is followed by an intraparticle densification process and smoothing of the interface, leading to the usual compact nonfractal, stable structures. The growth models proposed so far cannot account for the observed continuous changes of stages during the formation and growth of the particles. Copyright 1997 Academic Press. Copyright 1997Academic Press

Journal Article↗

PubMed2002

Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques.

The size distribution of molecules within an unfolded state of the N-terminal SH3 domain of drk (drkN SH3) has been studied by small-angle X-ray scattering (SAXS) and pulsed-field-gradient NMR (PFG-NMR) methods. An empirical model to describe this distribution in the unfolded state ensemble has been proposed based on (i) the ensemble-averaged radius of gyration and hydrodynamic radius derived from the SAXS and PFG-NMR data, respectively, and (ii) a histogram of the size distribution of structures obtained from preliminary analyses of structural parameters recorded on the unfolded state. Results show that this unfolded state, U(exch), which exists in equilibrium with the folded state, F(exch), under non-denaturing conditions, is relatively compact, with the average size of conformers within the unfolded state ensemble only 30-40% larger than the folded state structure. In addition, the model predicts a significant overlap in the size range of structures comprising the U(exch) state with those in a denatured state obtained by addition of 2 M guanidinium chloride.

Animals↗

PubMed2006

Nanostructure of the neurocentral growth plate: Insight from scanning small angle X-ray scattering, atomic force microscopy and scanning electron microscopy.

In this study, the experimental techniques scanning electron microscopy (SEM) including energy-dispersive X-ray analysis, atomic force microscopy (AFM) and scanning small angle X-ray scattering (SAXS) have been exploited to characterize the organization of large molecules and nanocrystallites in and around the neurocentral growth plate (NGP) of a pig vertebrae L4. The techniques offer unique complementary information on the nano- to micrometer length scale and provide new insight in the changes in the matrix structure during endochondral bone formation. AFM and SEM imaging of the NGP reveal a fibrous network likely to consist of collagen type II and proteoglycans. High-resolution AFM imaging shows that the fibers have a diameter of approximately 100 nm and periodic features along the fibers with a periodicity of 50-70 nm. This is consistent with the SAXS analysis that yields a cross-sectional diameter of the fibers in the range of 90 to 112 nm and a predominant orientation in the longitudinal direction of the NGP. Furthermore, we find inhomogeneities around 7 nm in the NGP by SAXS analysis. Moving towards the bone in the direction perpendicular to the growth plate, a systematic change in apparent thickness is observed, while the large-scale structural features remain constant. In the region of bone, the apparent thickness equals the mean mineral thickness and increases from 2 nm to approximately 3.5 nm as a function distance from the NGP. The mineral particles are organized as plates in a rather compact network structure. We have demonstrated that SEM, AFM and SAXS are valuable tools for the investigation of the organization of large molecules and nanocrystallites in the NGP and adjacent trabecular bone. Our findings will be an important basis for future work into identifying the defects on nanometer length scale responsible for idiopathic scoliosis and other growth-plate-related diseases.

Animals↗

PubMed1979

[Small angle X-ray scattering studies on the structure and symmetry of yeast pyruvate decarboxylase in solution].

The holo-enzyme of the pyruvate decarboxylase EC 4.1.1.1 isolated from brewer's yeast was studied by small-angle X-ray scattering. The point-group symmetry 222 deduced from electron microscopic investigations was confirmed for molecules in solution. The best approximation of the overall shape of the enzyme was reached by an homogeneous triaxial ellipsoid, with the half-axes of a = 2.47 nm, b = 5.08 nm and c = 8.0 nm. The ellipsoid is halved vertical to the a-axis, and both halves are turned from each other by about 30 degrees. As an explanation of the existence of four binding sites for Mg2+ and thiamine pyrophosphate on the dimeric molecule the hypothesis of a gene duplication is discussed.

Binding Sites↗

PubMed2000

Small-Angle X-Ray Scattering Studies on Nucleation Formation of Dextran Precipitation in the Presence of Boron.

In the present study, the nucleation formation process of dextran precipitation in the presence of boron was investigated by small-angle X-ray scattering (SAXS) techniques. The formation mechanism of aggregates or nuclei is very important in the initial step of crystallization. SAXS measurement is an excellent technique for observing these processes. The results of SAXS measurement suggest that boron, as a trace impurity, induces the aggregating of dextran molecules intermolecularly as a process in the nucleation formation of dextran precipitate nuclei and causes precipitation of dextran through an elongation process. These reactions occur readily at low boron concentrations. In fact, boron, which was detected at low levels in dextran solutions, was concentrated in the precipitates. Therefore, an aqueous solution of boron-free dextran should be resistant to precipitation. Copyright 2000 Academic Press.

Journal Article↗

PubMed1995

ATP-hydrolyzing excitation state of the reconstituted alpha 3 beta 3 complex of ATP synthase from the thermophilic bacterium PS3: structural characteristics shown by time-resolved small-angle X-ray scattering with synchrotron radiation.

The ATP-hydrolyzing excitation state of the alpha 3 beta 3 complex of the ATP synthase from the thermophilic bacterium PS3 was investigated using time-resolved small-angle X-ray scattering with synchrotron radiation. The results showed the presence of the alpha 3 beta 3 complex at a steady state during ATP hydrolysis when the alpha 3 beta 3 hexamer reacted with Mg-ATP. The radius of gyration of the complex in the steady state was significantly larger than that of the Mg-AMP-PNP-hexamer complex, indicating a conformational change to an expanded structure during catalysis. This alpha 3 beta 3 complex dissociated into alpha 1 beta 1 heterodimers with apparent first-order reaction kinetics after all the ATPs were converted to ADPs. In contrast, when the alpha 3 beta 3 complex reacted with Mg-ADP, the complex dissociated into dimers with apparent first-order reaction kinetics without showing the steady state of the complex. The dimers, however, re-associated into the hexamer when Mg-ATP was added. The results were well-explained by a computer simulation based on non-linear chemical dynamics, in which a reaction mechanism that incorporates the dynamic structure of the hexamer in the steady state was considered.

Adenosine Triphosphate↗

PubMed1978

Small-angle X-ray scattering on malate synthase from baker's yeast. The native substrate-free enzyme and enzyme-substrate complexes.

Malate synthase from baker's yeast has been investigated in solution by the small-angle X-ray scattering technique. Size, shape and structure of the native substrate-free enzyme and of various enzyme-substrate complexes have been determined. As the enzyme was found to be rather unstable against X-rays, several precautions as well as sophisticated evaluation procedures had to be adopted to make sure that the results were not influenced by radiation damage. These included use of low primary intensity, short time of measurement, the presence of high concentrations of dithiothreitol, combined use of the conventional slit-collimation system and the new cone-collimation system. 1. For the native substrate-free enzyme the following molecular parameters could be established: radius of gyration R = 3.96 +/- 0.02 nm, maximum particle diameter D = 11.2 +/- 0.6 nm, radius of gyration of the thickness Rt = 1.04 +/- 0.04 nm, molecular weight Mr = 187000 +/- 3000, correlation volume Vc = 338 +/- 5 nm3, hydration x = 0.35 +/- 0.02 g/g, mean intersection length - l = 5.0 +/- 0.2 nm. Comparison of the experimental scattering curve with theoretical curves for various models showed that the enzyme is equivalent in scattering to an oblate ellipsoid of revolution rather than to a circular cylinder. The semiaxes of this ellipsoid are a = b = 6.06 nm and c = 2.21 nm. Thus with an axial ratio of about 1:0.36 the enzyme is of very anisometric shape. 2. Binding of the substrates (acetyl-CoA, glyoxylate) or the substrate analogue pyruvate causes slight structural changes of the enzyme. These changes are reflected mainly by a slight decrease of the radius of gyration (0.3--1.3%, as established both with the slit-smeared and the desmeared curves). Concomitantly there occurs a decrease of the maximum particle diameter and an increase of the radius of gyration of the thickness. These changes imply an increase of the axial ratio by 2.2--6.9%, i.e. substrate binding induces a decrease of anisometry. While the particle volume appears to be unchanged on binding glyoxylate or its analogue pyruvate, binding of acetyl-CoA causes slight changes of this parameter. In a similar manner the binding of acetyl-CoA leads to a slight enhancement of the molecular weight; this increase corresponds to the binding of 2.7 +/- 1 molecules of acetyl-CoA.

Acetyl Coenzyme A↗

PubMed2004

Small angle X-ray scattering studies and modeling of Eudistylia vancouverii chlorocruorin and Macrobdella decora hemoglobin.

Annelids possess giant extracellular oxygen carriers that exhibit a hexagonal bilayer appearance and have molecular masses of approximately 3.5 MDa. By small angle x-ray scattering (SAXS), Eudistylia vancouverii chlorocruorin and Macrobdella decora hemoglobin were investigated in solution. On the basis of the experimental SAXS data, three-dimensional models were established in a two-step approach (trial and error and averaging). The main differences between the complexes concern the structure of their central part and the subunit architecture. Usage of our SAXS models as templates for automated model generation (program DAMMIN) led to refined models that fit perfectly the experimental data. Special attention was paid to the inhomogeneous density distribution observed within the complexes. DAMMIN models without a priori information could not reproducibly locate low-density areas. The usage of templates, however, improved the results considerably, in particular by applying electron microscopy-based templates. Biologically relevant information on the presence of low-density areas and hints for their presumable location could be drawn from SAXS and sophisticated modeling approaches. Provided that different models are analyzed carefully, this obviously opens a way to gain additional biologically relevant structural information from SAXS data.

Animals↗