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Evaluation of small-angle x-ray scattering data of a Raney-type Ni catalyst with computer simulation.

A reverse Monte Carlo-type simulation method was developed for the evaluation of anomalous small-angle x-ray scattering data of a Raney-type Ni catalyst. Based on other experimental data the catalytic Ni particles were modeled as small crystalline cylinders dispersed in the matrix. The average size of the Ni particles and their pair-correlation function were determined. Despite the unknown density of the catalyst, it is shown that each particle has about 2 neighbors in the first neighboring shell independent of the modeling density, and the position of the first peak of the pair-correlation function does not depend on the modeling density. A method was elaborated to get reasonable performance of the Reverse Monte Carlo-type simulation. The scattered intensity was calculated on the basis of probe scattering atoms put inside the cylinders. The effects of the omission of the real number of the atoms, the unknown density, the lack of normalization and the uncertainties in the cross sections were unified in two constants that were determined during the simulation. The method can be used for nanoparticles with other shape, where analytic form factors are complicated, and it may be powerful in the investigation of the usually neglected or simplified inter-particle structure of these systems.

Journal Article↗

Small-angle X-ray scattering on the ChemMatCARS beamline at the Advanced Photon Source: a study of shear-induced crystallization in polypropylene.

The first ever time-resolved small-angle X-ray scattering (SAXS) data from the undulator 15-ID-D beamline (ChemMatCARS) are presented. A 1.3 A (9.54 keV) X-ray beam was selected to study the structure development in a polypropylene sample during shear-induced crystallization. A Linkam CSS450 shear cell provided the temperature and shear control. The polypropylene was first melted and then quenched to the crystallization temperature, where a step shear was applied. The SAXS data were collected using a Bruker 6000 CCD detector, which provided images of excellent resolution. The SAXS images (with 180 degrees rotational symmetry) indicated that the polypropylene crystallizes with a high degree of anisotropy, and the lamellae are oriented perpendicular to the flow direction.

Crystallization↗

Structural studies of adenovirus type 2 by neutron and X-ray scattering.

Small-angle neutron and X-ray scattering have been used to investigate various aspects of the structural organization of adenovirus type 2. Neutron scattering allows the determination of the radial distribution of DNA and protein, which because of the highly icosahedral form of the virus allows it to be described in terms of three icosahedral shells. X-ray scattering shows that the distance between the major coat proteins (hexons) in the capsid is 100 +/- A. Evidence was also observed for an organization in the nucleoprotein core that gives rise to a maximum in the X-ray scattering at 1/29 A-1.

Adenoviruses, Human↗

[Determination of fractional and subfractional blood lipoprotein compositions with small angle X-ray scattering (a comparison with a biochemical method)].

Highly accurate and fast method for determination of quantitative and qualitative compositions of serum lipoprotein (LP) fractions and subfractions, using small-angle X-ray scattering on the "Siemens" difractometr, has been developed. The method allows to determine the concentrations of serum cholesterol (CH), triglycerides (TG), high-density lipoprotein (HDL)-CH, low-density lipoprotein (LDL)-CH, phospholipides (FL) and total lipids. It allows to determine the levels of CH, TG, FL in LP subfractions and concentrations of 5 very-low-density lipoprotein, intermedius-density lipoprotein, 3 LDL (large, intermedius and small dense particles) and 5 HDL subfractions. The method is based on the elaborated united model of all LP fractions and subfractions as a result of generalization and analysis of literature data about LP composition and size. New method was proved to be highly reproductive. Strong positive correlation exists between serum levels of CH, TG, HDL-CH determined by enzymatic biochemical and our methods. The method is simple to perform and of high diagnostic value, and can, therefore, be applied to clinical purposes.

Cholesterol↗

CD and small-angle x-ray scattering of silk fibroin in solution.

We investigated the structure of silk fibroin dissolved in water and in water-organic solvent mixtures by CD and small-angle x-ray scattering (SAXS). CD spectra indicated a disordered secondary structure in water and a beta-sheet conformation in aqueous organic solvents, such as methanol, dioxane, and trifluoroethanol (in trifluoroethanol a transient form evolving toward beta-sheet conformation was seen just after dissolution). The SAXS technique indicated the presence of fibroin particles of lamellar shape. The molecular weight was 188,000 daltons in water and 302,000 daltons in aqueous methanol.

Animals↗

Heat-induced unfolding of neocarzinostatin, a small all-beta protein investigated by small-angle X-ray scattering.

Neocarzinostatin is an all-beta protein, 113 amino acid residues long, with an immunoglobulin-like fold. Its thermal unfolding has been studied by small-angle X-ray scattering. Preliminary differential scanning calorimetry and fluorescence measurements suggest that the transition is not a simple, two-state transition. The apparent radius of gyration is determined using three different approaches, the validity of which is critically assessed using our experimental data as well as a simple, two-state model. Similarly, each step of data analysis is evaluated and the underlying assumptions plainly stated. The existence of at least one intermediate state is formally demonstrated by a singular value decomposition of the set of scattering patterns. We assume that the pattern of the solution before the onset of the transition is that of the native protein, and that of the solution at the highest temperature is that of the completely unfolded protein. Given these, actually not very restrictive, boundary constraints, a least-squares procedure yields a scattering pattern of the intermediate state. However, this solution is not unique: a whole class of possible solutions is derived by adding to the previous linear combination of the native and completely unfolded states. Varying the initial conditions of the least-squares calculation leads to very similar solutions. Whatever member of the class is considered, the conformation of this intermediate state appears to be weakly structured, probably less than the transition state should be according to some proposals. Finally, we tried and used the classical model of three thermodynamically well-defined states to account for our data. The failure of the simple thermodynamic model suggests that there is more than the single intermediate structure required by singular value decomposition analysis. Formally, there could be several discrete intermediate species at equilibrium, or an ensemble of conformations differently populated according to the temperature. In the latter case, a third state would be a weighted average of all non native and not completely unfolded states of the protein but, since the weights change with temperature, no meaningful curve is likely to be derived by a global analysis using the simple model of three thermodynamically well-defined states.

Calorimetry, Differential Scanning↗

Observation of RecA protein monomer by small angle X-ray scattering with synchrotron radiation.

RecA protein is capable of forming homo-oligomers in solution. The oligomeric and monomeric states of Thermus thermophilus RecA protein were studied by small angle X-ray scattering, a direct method used to measure the overall dimensions of a macromolecule. In the presence of 3 M urea or 0.2 M lithium perchlorate, RecA dissociates from higher oligomeric states to form a hexamer with a radius of gyration (R(g)) of 52 A. The value of R(g) decreased to 36 A at a higher lithium perchlorate concentration (1.0 M). The zero angle intensity, I(0), was consistent with the identification of the former state as a hexamer and the latter as a monomer.

Crystallography, X-Ray↗

In situ studies of monosaccharide gelation using the small-angle X-ray scattering time-resolved method.

The process of gelation of one of the monosaccharides, alpha-galactose-based gelator, with benzene as a solvent, has been studied. Small-angle X-ray scattering (SAXS) synchrotron time-resolved measurements were performed throughout the gelation process. The obtained SAXS measurements were elaborated using such methods as the fractal analysis, Fourier transform to get distance distribution functions, and simulation of a cluster model. We obtained the picture of the mesostructure development from the sol state to the gel state. Our results indicate that the fractal-type aggregates exist in the sol and the process of gelation is accompanied by the structural transition. This transition causes the aggregates to become smaller and denser, and their shapes differ from those of the sol. The complex method of SAXS data treatment we established seems to be a useful tool also for further studies of monosaccharide gelation.

Algorithms↗

Self-assembling process of cylindrical virus coat proteins as observed by synchrotron small-angle X-ray scattering.

The self-assembly process of cucumber green mottle mosaic virus (CGMMV) protein and tobacco mosaic virus (TMV) protein was examined by the thermodynamic analysis of small-angle X-ray scattering (SAXS) data. Each polymerization step of the coat proteins was assumed to be specified by a single equilibrium constant, and the equilibrium constant was evaluated by fitting the size and shape of the constituents observed by SAXS to those calculated from an assumed polymerization scheme. The logarithmic plots of the equilibrium constant against the inverse of temperature were fitted with a straight line at each buffer concentration and the thermodynamic quantities were evaluated from its intercept (yielding entropy) and slope (yielding enthalpy). The enthalpy and entropy values of TMV protein were found to be independent of buffer concentration, whereas those of CGMMV protein depended strongly on buffer concentration. In the limit, as ionic strength tends to infinity, both the enthalpy and entropy values of CGMMV protein approach those of TMV protein. The higher negative surface charge of CGMMV protein is considered to be responsible for the formation of stable single-layered disks, and for the slow polymerization process even at higher temperature and higher buffer concentrations.

Biopolymers↗

Dynamical self-assembly of nanocrystal superlattices during colloidal droplet evaporation by in situ small angle x-ray scattering.

The nucleation and growth kinetics of highly ordered gold nanocrystal superlattices during the evaporation of nanocrystal colloidal droplets was elucidated by in situ time-resolved small-angle x-ray scattering. We demonstrated for the first time that the evaporation rate can affect the dimensionality of the superlattices. The formation of two-dimensional nanocrystal superlattices at the liquid-air interface of the droplet has exponential growth kinetics that originates from interface crushing.

Journal Article↗

Small-angle X-ray scattering studies of tryptophan synthase from Escherichia coli and its alpha and beta 2 subunits.

The alpha and beta 2 subunits of tryptophan synthase were investigated by small-angle X-ray scattering. The molecular parameters are: radius of gyration, alpha: 1.95 nm, beta 2: 3.01 nm; maximum particle diameter, alpha: 5.8 nm, beta 2: 10.5 nm; and hydrated volume, alpha: 60 nm3, beta 2 160 nm3. The shape of the alpha subunit can best be described by a circular cylinder, slightly tapered at one end. An elongated elliptical cylinder with its cross section larger in the middle than at the ends was found to be a model equivalent in scattering to the beta 2 subunits. The alpha 2 beta 2 enzyme complex was found to have a radius of gyration of 4.01 nm, a maximum length of 13.5 nm, and a hydrated volume of 270 nm3. No satisfactory fit of the scattering data was obtainable by mere apposition of the models of the alpha and beta 2 subunits. Two cylinders overlapping laterally fit the experimental data considerably better, suggesting changes in the conformation of the subunits on forming the alpha 2 beta 2 complex.

Bacterial Proteins↗

Molecular organization of human plasma alpha 2-macroglobulin and its trypsin complexes. A small-angle x-ray scattering investigation.

The molecular organization of human plasma alpha 2-macroglobulin (alpha 2M), and its 1:1 and 1:2 trypsin complexes, have been investigated using the small-angle x-ray scattering method. All the experimental data can be explained by the same basic model, consisting of three oblate-shaped domains arranged in a sandwich-like structure. Each of the larger peripheral domains consists of two parallel elliptic cylinders associated side-by-side, whereas the smaller central domain consists of just one elliptic cylinder. In the native molecule the three domains are separated by regions of low protein density. Upon trypsin binding the dimensions of the four peripheral cylinders remain unchanged, but their positioning in space is reorganized so that the whole molecule becomes more compact. The model thus offers a plausible explanation for the mechanism of inactivating of the protease by entrapping it between the two larger domains. By comparing the shape and dimensions of the total molecule with those determined for the half-molecular fragment, obtained after reducing the intersubunit disulfide bonds, we propose that the fragment consists of just one of the peripheral domains plus half of the central domain. Different projections of the model are consistent with the electron micrographs of alpha 2M given in the literature. The model can also explain many of the physical and chemical properties recorded for alpha 2M and its protease complexes.

Disulfides↗

Order and orientation control of mesoporous silica films on conducting gold substrates formed by dip-coating and self-assembly: a grazing angle of incidence small-angle X-ray scattering and field emission scanning electron microscopy study.

Grazing-angle of incidence small-angle X-ray scattering (GISAXS) and high-resolution field emission scanning electron microscopy have been used to characterize the mesophase symmetry, orientation, and long-range order in PEO20-PPO70-PEO20 (Pluronic P123) templated mesoporous silica thin films on conducting gold substrates as a function of silica-to-ethylene oxide (Si/EO) block ratio and relative humidity (RH). The films are formed by dip-coating followed by evaporation-induced self-assembly under tightly controlled RH. The general evolution of the mesophase follows the trends that are expected based on shape factors due to swelling of the PEO block. However, changes in orientation of the nanostructure relative to the substrate and the degree of long-range order are found to depend on Si/EO ratio. These effects are likely due to the dynamics of evaporation and self-assembly. Generally, at Si/EO ratios lower than 3.29, the films contained regions where the nanostructure was not oriented relative to the plane of the substrate. However, for Si/EO ratios greater than 3.62, conditions were found where the nanostructure of the film was highly oriented relative to the plane of the substrate. This is true over the range of RH studied, independent of the nanostructure symmetry. For low Si/EO ratios at the highest RH levels, the films were composed of a mixture of spherical and cylindrical pores. At high Si/EO ratios and high RH levels, the films had a highly oriented R-3m nanostructure but displayed streaking perpendicular to the substrate in the Bragg spots on GISAXS patterns. This streaking is interpreted as faulting along planes parallel to the substrate.

Journal Article↗

Determination of the topological shape of integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria in the detergent solution by small-angle X-ray scattering.

The topological shape of the integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria Rhodobacter spheroides 2.4.1 in detergent solution has been determined from synchrotron small-angle X-ray scattering data using direct curve-fitting by the ellipsoid, ab initio shape determination methods of simulated annealing algorithm and multipole expansion, respectively. The results indicate that the LH2 protein in aqueous solution is encapsulated by a monolayered detergent shell. The detergent-stabilized structure has the shape of an oblate plate, with a thickness of 40 A, a long axis of 110 A, and a short axis of 85 A. After correction for the detergent shell, the shape of the LH2 core is also an oblate plate with a height of 40 A, a long axis of 80 A, and a short axis of 55 A. In contrast to the cylindrical crystal structure with a height of 40 A and a diameter of 68 A, the molecular shape of the LH2 complex in detergent solution clearly deviates from the ringlike crystal structure, with an eccentricity found to be 0.59-consistent with the result of single molecular spectroscopy study of the isolated single LH2 molecules.

Algorithms↗

Shape and volume of fragments Fab' and (Fab')2 of anti-poly(D-alanyl) antibodies in the presence and absence of tetra-D-alanine as determined by small-angle x-ray scattering.

The conformation of two fragments derived from anti-poly(D-alanyl) antibodies, the divalent fragment (Fab')2 and the monovalent fragment Fab', was studied by small-angle X-ray scattering before and after interaction with the tetra-D-alanine amide hapten. More than 90% of the combining sites were occupied by the hapten. No significant changes were observed in the volume or in the radius of gyration, with either of the fragments. This contrasts with the significant decrease in these two parameters found upon reacting the hapten with intact anti-poly(D-alanyl) antibodies (I. Pilz, O. Kratky, A. Licht, and M. Sela (1973), Biochemistry 12, 4998). For Fab', the radius of the whole particle was found to be 3.48 nm in the absence of the hapten and 3.46 nm in its presence, the radius of gyration of the cross-section was 1.37 nm without hapten and 1.38 nm in its presence, and the volume of the particle was 98 nm3 in the absence of the hapten and 91 nm3 in its presence. For (Fab')2 the respective values were 5.06 and 5.05, 1.38 and 1.37, and 182 and 182. These results suggest that a conformational change occurs within the antibody molecule, but not within its Fab fragment, upon reaction with the tetraalanine hapten.

Alanine↗

Mineralized microstructure of calcified avian tendons: a scanning small angle X-ray scattering study.

The micrometer level spatial distribution of the size, shape, and orientation of mineral crystallites in the calcifying matrix of tendons near the edge of the mineralizing front was investigated by scanning small angle X-ray scattering using synchrotron X-ray radiation. Using a special microbeam arrangement enabling 20 microm beam resolution and short measurement times, linear diffraction scans were made on sections from the normally calcifying tendons (tibialis cranialis) from the domestic turkey, which calcify in the distal to proximal direction. A change in shape and arrangement of mineral crystals was observed within the first 200 microm of the mineralization front, and the mineral crystal distribution was highly anisotropic with crystals aligned parallel to the fiber axis. In a cross-section of the tendon cut at right angles to the fiber axis, the orientation distribution of crystals was not azimuthally symmetric, and showed a small but nonzero anisotropy and a continuous change in mean orientation angle across the width of the tendon cross-section.

Animals↗

Biophysical characterization of the influence of salt on tetrameric SecB.

SecB is a tetrameric chaperone, with a monomeric molecular mass of 17 kDa, that is involved in protein translocation in Escherichia coli. It has been hypothesized that SecB undergoes a conformational change as a function of the salt concentration. To gain more insight into the salt-dependent behavior of SecB, we studied the protein in solution by dynamic light scattering, size exclusion chromatography, analytical ultracentrifugation, and small angle neutron scattering. The results clearly demonstrate the large influence of the salt concentration on the behavior of SecB. At high salt concentration, SecB is a non-spherical protein with a radius of gyration of 3.4 nm. At low salt concentration the hydrodynamic radius of the protein is apparently decreased, whereas the ratio of the frictional coefficients is increased. The protein solution behaves in a non-ideal way at low salt concentrations, as was shown by the analytical ultracentrifugation data and a pronounced interparticle effect observed by small angle neutron scattering. A possible explanation is a change in surface charge distribution dependent on the salt concentration in the solvent. We summarize our data in a model for the salt-dependent conformation of tetrameric SecB.

Bacterial Proteins↗

Small-angle x-ray scattering of high- and low-affinity heparin.

Solution characterization of heparin with high affinity (HA) and low affinity (LA) for antithrombin III was performed using the methods of small-angle x-ray scattering (SAXS), viscometry, and aqueous gel permeation chromatography (GPC). SAXS provided various topological parameters including the radius of gyration ([S2]1/2), radius of gyration of cross-section ([S2]q1/2), persistence length (a*), contour length (L), and mass parameters, e.g., overall molecular mass (Mr), and mass per unit length (Mq). The molecular weights of HA and LA pig mucosal heparins were found to be 14,900 and 11,500 and the respective radii of gyration were 40.1 and 33.6 A. The persistence lengths of HA and LA were 21.3 and 20.3 A, respectively. These parameters were compared to SAXS data of heparin [S. S. Stivala, M. Herbst, O. Kratky, and I. Pilz (1968) Arch. Biochem. Biophys. 127, 795-802] fractionated according to molecular weight only. It was found that the various experimental values of this heparin lie somewhere in between those of HA and LA heparins. It appears that there are no appreciable differences in the physico-chemical properties, including conformation, among the heparins in H2O at 25 degrees C.

Animals↗