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PubMed2004

In situ shear investigation of the Synperonic A7-water system by small-angle X-ray scattering and freeze fracture.

A shear cell was constructed in two variants for simultaneous small-angle X-ray scattering and freeze fracture. Using this cell, the changes in the layer structure and the domain formation of the Synperonic A7-water system were investigated under shear. The reconstructions of both the layer and domain structures were not observed in the steady state after 1 h (following a 2 h long shear period). Destruction of the lamellar arrangement and formation of aggregates occurred during the stress. It was concluded that the tixotropic behavior originates rather from the change of the domain structure with a typical size range of microm than from the changes of the inner structure of domains with lamellar arrangement.

Journal Article↗

PubMed2005

Fold recognition aided by constraints from small angle X-ray scattering data.

We performed a systematic exploration of the use of structural information derived from small angle X-ray scattering (SAXS) measurements to improve fold recognition. SAXS data provide the Fourier transform of the histogram of atomic pair distances (pair distribution function) for a given protein and hence can serve as a structural constraint on methods used to determine the native conformational fold of the protein. Here we used it to construct a similarity-based fitness score with which to evaluate candidate structures generated by a threading procedure. In order to combine the SAXS scores with the standard energy scores and other 1D profile-based scores used in threading, we made use both of a linear regression method and of a neural network-based technique to obtain optimal combined fitness scores and applied them to the ranking of candidate structures. Our results show that the use of SAXS data with gapless threading significantly improves the performance of fold recognition.

Computational Biology↗

PubMed2004

On the use of grazing-incidence small-angle X-ray scattering (GISAXS) in the morphological study of ion-implanted materials.

Grazing-incidence small-angle X-ray scattering has become a widely used technique for the morphological analysis of surface systems. Here it is show how this technique can be applied to a buried system, like metallic clusters in glass obtained by ion implantation. The optimization of the data-collection geometry is described as well as the details of the quantitative data analysis. An experimental example on Cu + Au-implanted glasses shows the potentiality of the technique.

Journal Article↗

PubMed1998

Lumbricus terrestris hemoglobin: a comparison of small-angle x-ray scattering and cryoelectron microscopy data.

The quaternary structure of Lumbricus terrestris hemoglobin was investigated by small-angle x-ray scattering (SAXS). Based on the SAXS data from several independent experiments, a three-dimensional (3D) consensus model was established to simulate the solution structure of this complex protein at low resolution (about 3 nm) and to yield the particle dimensions. The model is built up from a large number of small spheres of different weights, a result of the two-step procedure used to calculate the SAXS model. It accounts for the arrangement of 12 subunits in a hexagonal bilayer structure and for an additional central unit of clylinder-like shape. This model provides an excellent fit of the experimental scattering curve of the protein up to h = 1 nm-1 and a nearly perfect fit of the experimental distance distribution function p(r) in the whole range. Scattering curves and p(r) functions were also calculated for low-resolution models based on 3D reconstructions obtained by cryoelectron microscopy (EM). The calculated functions of these models also provide a very good fit of the experimental scattering curve (even at h > 1 nm-1) and p(r) function, if hydration is taken into account and the original model coordinates are slightly rescaled. The comparison of models reveals that both the SAXS-based and the EM-based model lead to a similar simulation of the protein structure and to similar particle dimensions. The essential differences between the models concern the hexagonal bilayer arrangement (eclipsed in the SAXS model, one layer slightly rotated in the EM model), and the mass distribution, mainly on the surface and in the central part of the protein complex.

Animals↗

PubMedDate not supplied

[On the supramolecular structure of eye lens crystalline. A study by small-angle x-ray scattering].

The supramolecular structure of clystallins from bovine and frog eye lens tissues was studied by small-angle X-ray scattering. The measurements were carried out at different orientations of the lens tissue on a diffractometer equipped with a coordinate detector with point collimation of the X-ray beam. The results indicate that crystallins occur in the lens in different structural states. One state is characterized by a small-angle diffraction maximum in the range of Bragg's distances D-15-22 nm, which is explained by a near order of macromolecular complexes of crystallins (alpha-crystallin), whereas for the other state, small-angle diffraction maxima in the range D-15-22 nm are not observed. The assumption is made that the second state is related to a homogeneous distribution of crystallin polypeptides in the lens and that the transition from this state to the state with the near order of macromolecular complexes may be due to the chaperone activity of these proteins.

Animals↗

PubMed1996

Application of the small-angle X-ray scattering technique for the study of two-step equilibrium enzyme-substrate interactions.

The small-angle x-ray scattering (SAXS) technique is used for the investigation of two-stage equilibrium macromolecular interactions of the enzyme-substrate type in solution. Experimental procedures and methods of analyzing the data obtained from SAXS have been elaborated. The algorithm for the data analysis allows one to determine the stoichiometric, equilibrium, and structural parameters of the enzyme-substrate complexes obtained. The thermodynamic characteristics for the formation of complexes of double-stranded oligonucleotide with Eco dam methyltransferase (MTase) have been determined and demonstrate a high cooperativity of MTase binding when the ternary complex containing the dimeric enzyme is formed. The structural parameters (Rg, Rc, semiaxes) have been determined for free enzyme and polynucleotides and of enzyme-substrate complexes, indicating structural rearrangements of the enzyme in the interaction with substrates.

Algorithms↗

PubMed2003

Small-angle x-ray scattering studies of metastable intermediates of beta-lactoglobulin isolated after heat-induced aggregation.

Small-angle x-ray scattering was used for studying intermediate species, isolated after heat-induced aggregation of the A variant of bovine beta-lactoglobulin. The intermediates were separated in two fractions, the heated metastable dimer and heated metastable oligomers larger than the dimer. The pair distance distribution functions for the two intermediate fractions as well as for the native protein have been obtained by indirect Fourier transformation. In addition, the scattering intensity data for samples of the native protein at different concentrations were fitted using a combination of monomer and dimer form factors, which provides an estimate of the amount of monomer in solutions. By subtracting the contribution from the monomer, the scattering intensity from the dimer of the native protein can be determined and compared with the results for the metastable dimer. An ellipsoidal model was used to fit the data for the metastable dimer, and for comparison the same analysis was performed on the dimer of the native protein. The results show that the metastable dimer is more elongated than the dimer of the native protein and it occupies a volume 1.4-fold larger, in agreement with a more loose, partially unfolded conformation. The same ellipsoidal model was used to analyze the data for the fraction of larger metastable oligomers. In this case, an even more elongated ellipsoid was obtained, suggesting a linear association of monomers in the oligomers.

Animals↗

PubMed2001

Head-to-tail and side-by-side oligomerization of human carbonic anhydrase II: a small angle X-ray scattering study.

Solvent-induced directional aggregation of human carbonic anhydrase II (hCA) was studied by small angle X-ray scattering and fluorescence and fourth-derivative ultraviolet absorption spectroscopy. We propose that hCA at 5 mg ml(-1) in pure water forms head-to-tail oligomers built up, on average, by four to five monomers. At higher protein concentrations, the oligomers associate pair-wise and side-by-side. Spectroscopic evidence suggests that the subunits forming the aggregates are tightly folded, but with a structure that differs, at least locally, from the native state. A more complex aggregation pattern was observed under solvent conditions that favor the removal of zinc from the enzyme-active site, conditions under which the subunits are significantly less compact than in water. hCA may provide a useful model to investigate the effects of additives and genetic manipulation on protein aggregation.

Binding Sites↗

PubMedDate not supplied

Small angle X-ray scattering and electron cryomicroscopy study of actin filaments: role of the bound nucleotide in the structure of F-actin.

Actin filaments (F-actin) complexed to various nucleotides (ADP (adenosine diphosphate) ADP-P(i) (P(i), inorganic phosphate), and ADP-BeF3- (BeF3-, beryllium fluoride)) have been studied by small angle X-ray scattering and electron cryomicroscopy. The small angle X-ray scattering data show that the value of the cross-radius of gyration (2.55 +/- 0.15 nm) and the mean helical symmetry of the filaments are independent of the nature of the bound nucleotide. The scattering profiles of all the F-actin suspensions exhibit secondary maximal located at similar positions. However, the intensities of the secondary maxima depend upon both the protein concentration and the type of nucleotide bound to the F-actin. These variations indicate that F-actin has different properties (such as its tendency to aggregate and the structure of the filament), which depend upon the type of nucleotide bound. Electron cryomicroscopy of vitrified suspensions shows that F-actin may have different conformations. The nonequatorial layer lines, which constitute the Fourier transforms of the filament images, have different signal to noise ratios depending on the type of nucleotide bound to the actin. The 3-D reconstructions of the actin filaments show an inner and outer domain. In the maps, the visibility of the outer domain depends upon the type of nucleotide bound to the actin. It respectively increases for ADP-P(i), ADP, and ADP-BeF3-. We attribute these differences to the disorder of the filaments, which in turn depends upon the nucleotide bound. These variations in disorder imply that there are structural changes (contacts, structure, or orientation) in the actin subunits forming the filaments. These changes may have an important role in the motility processes in which actin is involved.

Actins↗

PubMed2005

Sodium chloride and ethanol induced sphere to rod transition of triblock copolymer micelles.

Dynamic light scattering (DLS), small-angle neutron scattering (SANS), and viscosity studies have been carried out to examine the influence of NaCl and ethanol on the structure of triblock copolymer [(EO)20(PO)70(EO)20] (EO = ethylene oxide; PO = propylene oxide) micelles in aqueous medium. The studies show that while the pure triblock copolymer solutions do not show any significant growth of the micelles on approaching the cloud point, the presence of a small amount of ethanol (5-10%) induces a sphere to rod shape transition of micelles at high temperatures. Interestingly, this ethanol induced sphere to rod transition of micelles can be brought down to room temperature (25 degrees C) with the addition of NaCl. It is also found that NaCl alone cannot induce such sphere to rod transitions and excess ethanol suppresses them by increasing their transition temperature.

Journal Article↗

PubMed2002

BPTI liquid-liquid phase separation monitored by light and small angle X-ray scattering.

In the field of protein crystallization, a better knowledge of the nucleation process is essential to control the nucleation rate, the growth and therefore the size and the quality of crystals. With that aim, it becomes clear that the important stage is the determination of the protein phase diagram. We highlighted and investigated the bovine pancreatic trypsin inhibitor (BPTI) binary liquid-liquid phase separation in 350 mM KSCN solutions as a function of temperature. We measured the low concentration part of the binodal curve using light scattering and optical microscopy. We show, from small angle X-ray scattering experiments, that the high concentrated phase sediments in the bottom of the capillary and we analysed the low concentrated phase in terms of monomers/decamers equilibrium.

Animals↗

PubMed1978

Small angle x-ray scattering studies on adenovirus type 2 hexon.

Adenovirus type 2 hexons have been studied in solution by small angle X-ray scattering, and the following molecular parameters determined: radius of gyration (Rg) = 4.9 nm, molecular weight (M) = 310.000, invariant volume (Vinv) = 630 mn3, maximal distance (Dmax) = 14.5--15.5 nm. A diffraction pattern was obtained up to an angular increment of h = 2.5 nm-1. Various models for the hexon have been explored by calculating the diffraction pattern from the Debye formula for 1200 spheres arranged to define the scattering volume of each model. Models were first built according to electron micrographic results. Later, preliminary results of a crystallographic study were used for model building. The experimental pattern and the pattern resulting from the model determined by crystallographic methods were compared and showed good agreement.

Adenoviridae↗

PubMed2004

Small-angle X-ray scattering and electron paramagnetic resonance study of the interaction of bovine serum albumin with ionic surfactants.

Small-angle X-ray scattering (SAXS) and electron paramagnetic resonance (EPR) techniques have been used to monitor the interaction of bovine serum albumin (BSA) with ionic surfactants such as anionic sodium dodecyl sulfate (SDS), zwitterionic N-hexadecyl-N,N-dimethyl-3-ammonium-1-propane sulfonate (HPS), and cationic cethyltrimethylammonium chloride (CTAC) at pH 7.0. The SAXS results have shown that in the presence of 5 mM SDS and HPS the radius of gyration (Rg) almost does not change as compared to the BSA free-surfactant solution; its value is ca. 30 Angstroms. In the presence of 5 mM CTAC the SAXS data indicate the presence of a particle with a Rg of at least 63 Angstroms, suggesting that in this case, a kind of protein aggregation takes place. In the presence of SDS and HPS surfactants at concentrations above 10 mM, a characteristic broad peak in the region of 0.12-0.18 Angstroms(-1) indicates the presence of micelle-like aggregates in solution. The SAXS curves are consistent with the "pearl necklace" model, where micelle-like aggregates are randomly distributed around the polypeptide chain. EPR results using 5-DSA and 16-DSA spin labels show that in the presence of BSA the EPR spectra are composed of two label populations, one contacting the protein and a second one due to label localization in the micelles. Evidence is also obtained for a competition of the surfactants with the spin labels for the high-affinity binding sites of the stearic acid spin labels as monitored by changes in the fractions of the two label populations as the surfactant concentration is increased. The effect of SDS seems to be stronger in the sense that increased SDS concentration leads to a complete transfer of spin labels from close protein contact sites to micelles, while for HPS, a significant immobilization of probe apparently remains even at higher surfactant concentrations. These two techniques are quite useful since SAXS monitors the overall properties of the scattering particle, while EPR gives information on the dynamics inside this particle and associated with label localization and motion.

Animals↗

PubMed2006

Localization of dibromophenol in DPPC/water liposomes studied by anomalous small-angle X-ray scattering.

The localization of 2,4-dibromophenol molecules along the bilayer normal was investigated by anomalous small-angle X-ray scattering (ASAXS) with synchrotron radiation. The ASAXS measurements, executed at three different energies, provide the separation of the scattering of the bromine atoms of dibromophenol molecules from that of the whole system. Using a full q-range model, the localization of the dibromophenol molecules was characterized at a lower (0.1) and a higher (1) dibromophenol/lipid molar ratio corresponding to the gel and to the interdigitated phases of the vesicle matrix, respectively.

Letter↗

PubMed2005

Small angle x-ray scattering of a supercritical electrolyte solution: the effect of density fluctuations on the hydration of ions.

Synchrotron small angle x-ray scattering measurements on water and zinc bromide ZnBr2 aqueous solutions were carried out from ambient to supercritical conditions. For both systems several isobars (between 285 and 600 bars) were followed beyond the critical isochore. The data were analyzed through an Ornstein-Zernike formalism in terms of correlation length and null angle structure factor. The results for pure water are in agreement with previously published values. Solutions of different electrolyte concentrations were studied. In each case, the values of the correlation length and null angle structure factor are larger than those of pure water. This effect is more pronounced for higher concentrations and/or for pressure closer to the critical point of pure water. This is in agreement with the shift of the critical point determined in the literature for NaCl solutions. Comparing these results to previous x-ray absorption measurements carried out on identical samples we propose the following two step sequence for ionic hydration up to supercritical conditions: (1) from ambient to about 300 degrees C, an increase of ion pairing and formation of multi-ionic complexes which can be correlated to the decrease of the dielectric constant; (2) an enhancement of the local solvation shell of ions due to the onset of the thermal density fluctuations at high temperature, leading to a screening effect between ions and inhibiting the ion pairing processes.

Journal Article↗

PubMed1978

Studies on the structure of rat-liver polysomes by small-angle X-ray scattering.

The spatial structure of rat liver polysomes in dilute solution has been studied by the small-angle X-ray scattering technique. The distance between the mass centres of neighbouring ribosomes on the mRNA molecule is 35 nm, and the distance from next-but-one neighbour, about 55 nm. The spatial arrangement of the ribosomes on the polysome is compact; stretched configurations can be ruled out. The best model is a solenoid with six ribosomes per turn and a pitch of about 33 nm. The greatest diameter of a polysome with eight ribosomes is 130 nm, the radius of gyration 34 nm.

Animals↗

PubMed1991

Structure of Colorado potato beetle lipophorin: differential scanning calorimetric and small-angle X-ray scattering studies.

The structure of lipophorin, isolated from hemolymph of the Colorado potato beetle, was investigated by differential scanning calorimetry (DSC) and small-angle X-ray scattering. The DSC heating curves of intact lipophorin showed endothermic peaks that were similar to peaks obtained with the hydrocarbon fraction isolated from this lipophorin. The observed peaks correlated with the transition of the hydrocarbons from an ordered into a more disordered state. Changes in structure of the lipophorin particles with increasing temperature were also observed by small-angle X-ray scattering studies. The structural organization of lipophorin was further elucidated by simulation analysis, using a three-layered symmetrical sphere as a model. These studies revealed that lipophorin from the Colorado potato beetle is a sphere with a maximum diameter of 175 A. The sphere is composed of three radially symmetrical layers of different electron densities. The outer layer (37.5-39.5 A in thickness) is composed of phospholipid, apolipophorin I, and part of apolipophorin II. The middle layer (5-10 A) contains diacylglycerol, the rest of apolipophorin II, and probably beta-carotene. The core of the particle (40-45 A) only contains hydrocarbons. This structure differs from another model, previously proposed for cockroach and locust lipophorins [Katagiri, C., Sato, M., & Tanaka N. (1987) J. Biol. Chem. 262, 15857-15861], in the small size of the middle layer. The volume of the middle layer correlated well with the low diacylglycerol content of this lipophorin.

Animals↗

PubMed2004

Small-angle static light scattering of concentrated silica suspensions during in situ destabilization.

The aggregation of concentrated aqueous silica suspensions is characterized by means of static light scattering. We use an in situ destabilization mechanism based on the enzyme-catalyzed hydrolysis of urea. This method enables us to continuously and homogeneously change the interparticle potential from repulsive to attractive without disturbing the aggregation process. Moreover, our electrostatically stabilized suspensions can be destabilized by two different methods. In the first method, the pH is shifted toward the isoelectric point of the particles ( Delta pH method), thereby leading to a decrease of their surface charge. In the second method, the ionic strength is continuously increased at constant pH ( Delta I method), leading to a compression of the electrical double layer around the charged particles. A laboratory-built flat-cell light-scattering instrument is used, which allows fast data acquisition and an adjustment of the sample cell thickness. To circumvent multiple scattering effects, we use a very small sample thickness ( approximately 13 microm). In addition, the refractive index difference between the aqueous phase and the particles is reduced by adding sucrose to the liquid phase of our suspensions. We are able to characterize the structural changes at the very early stages of the destabilization process, where no significant effects are yet detected in macroscopic rheological measurements. While during the Delta pH destabilization, the scattering curve shows significant changes only after some characteristic delay time, it changes continuously during the Delta I destabilization. The latter is attributed to the formation of a weak pre-gel structure in the suspensions, as a shallow secondary minimum appears in the interparticle potential. Data are evaluated by using a HMSA square-well structure factor model. Results are in good agreement with those predicted from DLVO theory.

Journal Article↗