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At least 19 recordsLinked to original sources

PubMed2005

Invalidity of deriving interparticle distance in clay-water systems using the experimental structure factor maximum obtained by small-angle scattering.

Small-angle X-ray scattering (SAXS) has been widely used to investigate the organization of clay colloids in response to the particle concentration and ionic strength of the suspending medium. In such investigations, measuring the interparticle distance and/or spacing is usually attempted. In random or short-range ordered clay-water systems, the interparticle distances are often derived from the experimental structure factor maximum; however, the validity of such practice has never been theoretically or experimentally evaluated. The experimental structure factors of several clay-water systems with and without polyphosphate treatment to block the edge charges of clay particles were obtained from SAXS data in order to understand the physical meaning of this property. The results show that the polyphosphate treatment eliminated the experimental structure factor maximum and that the particle concentration effects were correlated with the depression on the curve in a random clay-water system (e.g., illite and laponite). For clay particles with greater anisotropy (i.e., montmorillonite), polyphosphate treatment enhanced the ordering of clay layers at high particle concentrations forming long-range ordered crystals showing Bragg reflections. In this ordered system, distinctive and symmetrical peaks representing the interparticle spacing were obtained by using a Fourier transform of the scattering curves. Thus, we conclude that the experimental structure factor maximum is induced by the edge-face oriented interactions, which may not be in direct contact as in a house-of-cards structure, and the position of the maximum should not be interpreted as an averaged interparticle distance in a clay-water system unless particles orient along the same direction.

Journal Article↗

PubMed2005

Scattering structure factor of colloidal gels characterized by static light scattering, small-angle light scattering, and small-angle neutron scattering measurements.

The scattering structure factor of a colloidal gel in a q range of 5 orders of magnitude has been determined by combining static light scattering, small-angle light scattering, and neutron scattering measurements. It exhibits simultaneously two types of structure information: a mass fractal scaling within the clusters that constitute the gel and a surface fractal scaling for length scales larger than that of the clusters. Such scattering behavior can be well interpreted by the pair-correlation function proposed in the literature to model an ideal structure constituted of mass fractal objects inside surface fractal objects.

Journal Article↗

PubMed1974

X-ray small angle scattering. A new deconvolution method for evaluating electron density distributions from small angle scattering diagrams.

The direct determination of the electron density distributions of multilayered specimens with a small number of unit cells from X-ray small angle scattering experiments via the Q-function method of Hosemann and Bagchi includes the deconvolution of the so-called Q(o)-function, the generalized Patterson function of one unit cell. In this paper a new and direct deconvolution method on the basis of Fourier series is presented which is suitable for one-dimensional centrosymmetrical (or antisymmetrical) density distributions. A FORTRAN-program has been written which has an execution time of ca. 20 s on an UNIVAC 1106-computer. The procedure has been successfully tested on some convolution functions generated by membrane-type electron density distributions.

Computers↗

PubMed1977

Comparative neutron small-angle scattering study of small spherical RNA viruses.

Small-angle neutron scattering from solutions of small RNA viruses has been used to study protein-nucleic acid organisation. In the five viruses investigated the RNA is confined to a sphere of about 100 A radius, with a central hole (with one possible exception). The interpenetration of RNA and protein varies with viruses and seems to be related to the natrue of the forces stabilising the virus.

Coliphages↗

PubMed2000

Ligand-induced conformational changes in tissue transglutaminase: Monte Carlo analysis of small-angle scattering data.

Small-angle neutron and x-ray scattering experiments have been performed on type 2 tissular transglutaminase to characterize the conformational changes that bring about Ca(2+) activation and guanosine triphosphate (GTP) inhibition. The native and a proteolyzed form of the enzyme, in the presence and in the absence of the two effectors, were considered. To describe the shape of transglutaminase in the different conformations, a Monte Carlo method for calculating small-angle neutron scattering profiles was developed by taking into account the computer-designed structure of the native transglutaminase, the results of the Guinier analysis, and the essential role played by the solvent-exposed peptide loop for the conformational changes of the protein after activation. Although the range of the neutron scattering data is rather limited, by using the Monte Carlo analysis, and because the structure of the native protein is available, the distribution of the protein conformations after ligand interaction was obtained. Calcium activation promotes a rotation of the C-terminal with respect to the N-terminal domain around the solvent-exposed peptide loop that connects the two regions. The psi angle between the longest axes of the two pairs of domains is found to be above 50 degrees, larger than the psi value of 35 degrees calculated for the native transglutaminase. On the other hand, the addition of GTP makes possible conformations characterized by psi angles lower than 34 degrees. These results are in good agreement with the proposed enzyme activity regulation: in the presence of GTP, the catalytic site is shielded by the more compact protein structure, while the conformational changes induced by Ca(2+) make the active site accessible to the substrate.

Calcium↗

PubMed2005

A model for the three-dimensional structure of human plasma vitronectin from small-angle scattering measurements.

Small-angle X-ray scattering (SAXS) measurements were used to characterize vitronectin, a circulatory protein found in human plasma that functions in regulating cell adhesion and migration, as well as proteolytic cascades that affect blood coagulation, fibrinolysis, and pericellular proteolysis. SAXS measurements were taken over a 3-fold range of protein concentrations, yielding data that characterize a monodisperse system of particles with an average radius of gyration of 30.3 +/- 0.6 A and a maximum linear dimension of 110 A. Shape restoration was applied to the data to produce two models of the solution structure of the ligand-free protein. A low-resolution model of the protein was generated that indicates the protein to be roughly peanut-shaped. A better understanding of the domain structure of vitronectin resulted from low-resolution models developed from available high-resolution structures of the domains. These domains include the N-terminal domain that was determined experimentally by NMR [Mayasundari, A., Whittemore, N. A., Serpersu, E. H., and Peterson, C. B. (2004) J. Biol. Chem. 279, 29359-29366] and the docked structure of the central and C-terminal domains that were determined by computational threading [Xu, D., Baburaj, K., Peterson, C. B., and Xu, Y. (2001) Proteins: Struct., Funct., Genet. 44, 312-320]. This model provides an indication of the disposition of the central domain and C-terminal heparin-binding domains of vitronectin with respect to the N-terminal somatomedin B (SMB) domain. This model constructed from the available domain structures, which agrees with the low-resolution model produced from the SAXS data, shows the SMB domain well separated from the central and heparin-binding domains by a disordered linker (residues 54-130). Also, binding sites within the SMB domain are predicted to be well exposed to the surrounding solvent for ease of access to its various ligands.

Computational Biology↗

PubMed2000

Determination of the structure of tissue samples using X-ray small angle scattering.

X-ray small angle scattering has been used in material science for about 50 years. In diagnostic medicine, it has been applied for some years. The theoretical background is the diffraction of monochromatic X-rays by the electrons of small particles. The widening of the primary beam by those samples allows a conclusion regarding particle size, size distribution, and the form of the particles. The camera requires a well-defined and small X-ray beam which has to be entrapped exactly behind the sample. To date, the medical application has been carried out mainly by the comparison of the measured curve with that of standard samples. It can be suggested that in the near future its application in medicine will increase particularly with regard to in vivo measurements. For this purpose, new cameras will have to be developed. An exact evaluation of the result requires a thorough knowledge of the theoretical basis.

Breast↗

PubMed2005

Effective long-range attraction between protein molecules in solutions studied by small angle neutron scattering.

Small angle neutron scattering intensity distributions taken from cytochrome C and lysozyme protein solutions show a rising intensity at a very small wave vector Q, which can be interpreted in terms of the presence of a weak long-range attraction between protein molecules. This interaction has a range several times that of the diameter of the protein molecule, much greater than the range of the screened electrostatic repulsion. We show evidence that this long-range attraction is closely related to the type of anion present and ion concentration in the solution.

Animals↗

PubMed1986

Formation of actin dimers as studied by small angle neutron scattering.

Small angle neutron scattering has been used to study the dimensions of G-actin and the formation of low molecular weight actin oligomers under conditions where rapid polymerization does not take place. In the presence of 200 microM Ca2+, actin in solution consists of a single component with a radius of gyration (Rg) of 19.9 +/- 0.4 A, consistent with the known molecular dimensions of the G-actin molecule. In the presence of 50 microM Mg2+, however, formation of an actin species with a larger Rg occurs over a 4-h period. Multicomponent fits were tried and the data were best fit assuming two components, the monomer and a species with an Rg of 29 +/- 1 A. This latter value is consistent with the dimensions expected for certain actin dimers. The apparent dissociation constant for dimer formation is approximately 150 microM with forward and reverse rate constants of 6.0 X 10(-7) microM-1 s-1 and 8.8 X 10(-5) s-1, respectively. Kinetic fluorescence experiments show that the dimer formed in the presence of low levels of Mg2+ is a nonproductive complex which does not participate in the polymerization process. However, the addition of cytochalasin D to actin in the presence of 50 microM Mg2+ rapidly induces the formation of dimers, presumably related to cytochalasin's ability to nucleate actin polymerization.

Actins↗

PubMed1984

The shape of ribulose bisphosphate carboxylase/oxygenase in solution as inferred from small angle neutron scattering.

Small angle neutron scattering of both activated and deactivated hexadecameric ribulose bisphosphate carboxylase/oxygenase from spinach revealed that its structure in solution very closely resembles that determined for the deactivated crystalline enzyme from tobacco (Baker, T.S., Eisenberg, D., and Eiserling, F. (1977) Science 196, 293-295). Scattering from both forms of the enzyme in H2O most closely fits that expected from a hollow sphere with an outer radius of 56.4 A and inner radius of 14.3 A. In D2O the enzyme's scattering profiles more closely resembled those of a hollow cylinder with an axial ratio of approximately 1.06 and outer and inner radii of 46.7 and 12.9 A, respectively. Superpositioning of model structures showed that both models determined by neutron scattering correspond quite well to that inferred from x-ray diffraction and electron microscopy of the tobacco enzyme. Sedimentation velocity studies confirmed that no major conformational change occurs upon activation of the spinch carboxylase, both forms exhibiting a sedimentation coefficient, 8(20,w), of 17.8 S. Neutron scattering by activated and deactivated carboxylase from Rhodospirillum rubrum, a dimeric enzyme, best matched that predicted for a solid prolate ellipsoid or cylinder. The estimated dimensions of the model structures correspond strikingly well to those predicted for adjacent pairs of large subunits in the hexadecameric tobacco enzyme.

Molecular Weight↗

PubMed1989

Synchrotron X-ray scattering study of chromatin condensation induced by monovalent salt: analysis of the small-angle scattering data.

Small-angle X-ray scattering experiments were carried out on rat thymus chromatin in "native" and "H1-depleted" states at various NaCl concentrations using synchrotron radiation. From the analysis of cross-sectional Guinier plots, the radius of gyration of the cross section (Rc) and the mass per unit length (Mc) of native chromatin were evaluated. In the absence of NaCl, the cross section of chromatin filament has a radius of gyration of 3.44 nm, suggesting the structure corresponding to the "10 nm" filament. With increasing NaCl concentration, the Rc value increases steeply to 6.74 nm at 5 mM NaCl and then gradually to 8.82 nm at 50 mM NaCl, whereas the Mc value, which is determined relative to that of tobacco mosaic virus (TMV), increases steadily from 1.58 nucleosomes per 10 nm in the absence of NaCl to 7.66 nucleosomes per 10 nm at 50 mM NaCl. However, since calibration with TMV tends to overestimate the Mc value, the actual Mc values may be less than those values. Above about 40 mM NaCl, aggregation of chromatin is suggested. Similar analysis of H1-depleted chromatin confirmed that H1-depleted chromatin takes a more disordered structure than native chromatin at low ionic strength and does not undergo a definite structure change upon further addition of NaCl.

Animals↗

PubMed1991

Direct proof of a "more-than-single-layered" peptidoglycan architecture of Escherichia coli W7: a neutron small-angle scattering study.

A neutron small-angle scattering study was performed to determine the thickness and the scattering density profile of isolated peptidoglycan sacculi of Escherichia coli W7 in aqueous suspension (D2O). The maximum thickness (7 +/- 0.5 nm) of the sacculus from the exponential-phase cells was large enough to suggest the existence of a more-than-single-layered architecture. The experimental density profile across the thickness of the sacculus did not allow an unambiguous differentiation between a single-layered architecture characterized by completely extended peptide side chains projecting from the sugar strands or, alternatively, a partially triple layered structure. To resolve this ambiguity, sacculi were labeled with deuterated wall peptides. Comparison of the two experimental profiles indicated that the sacculus is more than single layered across its surface, with about 75 to 80% of its surface single layered and 20 to 25% triple layered.

Escherichia coli↗

PubMed1981

General shape and hapten-induced conformational changes of pig antibody against dinitrophenyl. A small-angle scattering study.

Pig antibodies against dinitrophenyl were studied by neutron small-angle scattering and X-ray small-angle scattering with particular attention to the analysis of cross-section plots and determination of the radii of gyration of cross-section. The experimentally determined molecular parameters Rg (radius of gyration), Rq1 and Rq2 (two different radii of gyration of cross-section characterizing every antibody sample) show that the shapes of the two antibody types, precipitating and non-precipitating, are similar. The non-precipitating antibody is slightly more compact. The parameters Rg, Rq1 and Rq2 of complexes of antibodies with the hapten, 8-dinitrophenyl-5,8-aza-4-oxo-octanoic acid, are smaller than those of the free antibody. This indicates that a conformational change is induced by the binding of the hapten. The character of the change of parameters is consistent with a view that the observed contraction of the molecule proceeds via similarity transformation. In order to design a model of a pig antibody molecule, isolated building blocks of the molecule, the Fab and Fc fragments, were first studied. A comparison of the scattering curves with various models of fragments showed, however, that the isolated fragments acquire in solution elongated rod-like shapes. Over 300 tentative models of the intact antibody molecule, built of small identical spheres, were constructed before a good fit with the experimental data was achieved. The most probable models have a cavity in the Fc part and the Fab parts are either fully extended or slightly bent downwards to the Fc part.

Animals↗

PubMed1990

Intercomparison of small biomolecules by gel filtration and small angle scattering.

This paper describes how small angle neutron scattering (SANS) can be used to confirm that gel filtration results are free of dimerization effects. After characterization by analytical gel filtration, concentrated solutions (in heavy water, D2O) of a cobra neurotoxin, a cytotoxin, and a cytotoxin analog are studied by SANS. Small differences in shape are shown to be discernible by means of least-square fits to ellipsoidal models. The parallel axis theorem is then invoked to assess dimerization levels statistically. The results are briefly discussed on the basis of function in relation to structure.

Cobra Neurotoxin Proteins↗

PubMed2006

Synchrotron radiation small angle scattering studies of thermal stability of xylanase XYNII from Trichoderma longibrachiatum.

Xylanase XYNII from Trichoderma longibrachiatum is a small protein of the molecular weight 21 kDa, belonging to the family 11 of glycosyl hydrolases, which catalyses hydrolysis of xylan. This article reports thermal stability study of xylanase XYN II conformation in the temperature range 15-65 degrees C by the small angle synchrotron radiation scattering. The study has been performed at different pH conditions: at pH 4.0 (below the physiological optimum of the enzyme activity) at pH 5.8 close to the optimum for enzymatic activity and at pH 8.0. The radius of gyration and the pair distance distribution function p(r) have been analyzed to characterize the changes of the enzyme conformation on heating. In the environment of the pH close to that of the optimum for the enzymatic activity, xylanase shows the greatest thermal stability and undergoes denaturation only above 55 degrees C. In the acidic and basic environments, the enzyme stability is much lower and denaturation begins at 45 degrees C. On the basis of the SAXS data, the shape of the xylanase molecule in solution in different temperatures has been reconstructed using ab initio method and program DAMMIN. The shape of the xylanase molecule at room temperature is similar to the right hand, which is typically observed for xylanase crystal structure. In higher temperatures (close to the enzyme activity optimum), the conformation of the right hand is loosened and half opened.

Endo-1,4-beta Xylanases↗

PubMed1999

Small-angle scattering by dislocations.

It is shown that the small-angle scattering of X-rays or neutrons by dislocations within a deformed metal, which are partially ordered into wall-like structures, is characterized by several factors. Principally these are associated with: (i) a single dislocation or dipole; (ii) the dislocation configuration in the plane of the wall; and (iii) the distribution of dislocations across the wall thickness. With the assumption of isotropic elasticity, small-angle scattering will be sensitive only to the edge components of the dislocations. The scattered intensity is dominated by scattering from dislocations that lie perpendicular to the scattering vector, q, and reaches a maximum when q is normal to the slip plane of these dislocations. Above a particular |q|, the scattered intensity is sensitive only to the total edge dislocation content of the scattering dislocations (i.e. scattering is incoherent), while, below this value, the scattering is dominated by how the dislocations are distributed in walls. For walls normal to their slip planes, the configuration factor will reflect the dislocation distribution in the plane of the wall, while, for walls parallel to their slip planes, the distribution in the thickness direction will be visible. Therefore, even though a deformed material is composed of complicated dislocation structures, only those segments conforming to these rather strict prescriptions will be singled out for scattering, and, by adjusting the beam/slip system geometry, many parameters of the microstructure can be determined experimentally.

Journal Article↗

PubMed1978

The structure of human-plasma low-density lipoprotein B. An X-ray small-angle scattering study.

1. X-ray small-angle scattering of human plasma lipoprotein B of the low-density fraction (rho = 1.016--1.060 g.cm-3) has been recorded to high precision at different electron density contrasts. 2. The overall structure of the particles is characterized by a quasi-spherical shape and radial symmetry. A maximum diameter of 23 nm and a molecular weight of 2.4 X 10(6) have been determined. 3. The internal structure is described in terms of a model consisting of spherical layers with different electron densities indicating that the neutral lipids are arranged in the core of the molecule up to a radius of about 8 nm surrounded by a monolayer of free cholesterol, phospholipids and protein. The neural lipids are shown to be in an ordered, liquid crystalline state at 4 degrees C and to undergo a thermotropic transition into a disordered state at higher temperatures.

Cholesterol↗

PubMed2006

A small-angle scattering study on equilibrium clusters in lysozyme solutions.

We use small-angle scattering experiments to investigate the structural properties of aqueous lysozyme solutions under conditions where the existence of equilibrium clusters has recently been demonstrated (Nature 2004, 432, 492). We also discuss the possible emergence of a low angle scattering contribution, which recently attracted interest due to its appearance in solutions of various proteins. We demonstrate that in lysozyme solutions under our experimental conditions such rising low q intensities can only be observed under special circumstances and can thus not be attributed to the existence of a universal long-range attraction. We then focus on the structural properties of the equilibrium clusters as a function of protein concentration, temperature, and ionic strength. We show that the experimental structure factors obtained from the scattering measurements exhibit the typical cluster-cluster peak q(c) reflecting the mean distance between charged clusters as well as a monomer-monomer peak q(m), which represents the nearest neighbor shell of monomers within a single cluster. The underlying principle for the formation of these structures is the coexistence of two opposing forces, a short-range attraction and a long-range repulsion due to residual charges. We can quantitatively analyze our scattering data by applying a simple equilibrium cluster model and calculate an average cluster aggregation number, N(c). The thus obtained cluster aggregation number increases linearly with volume fraction. We also observe an increasing N(c) as temperature decreases and as the screening of residual charges increases. We point out the importance of the existence of equilibrium clusters and the universality of this phenomenon for self-assembling processes observed in nature. Finally, we discuss the limitations of our simple globular cluster model in view of recent findings from computer simulations.

Diffusion↗