SEARCH · PubMed Health

Results for “Scattering, Small Angle”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46Linked to original sources

PubMed2005

The C-terminal (331-376) sequence of Escherichia coli DnaJ is essential for dimerization and chaperone activity: a small angle X-ray scattering study in solution.

DnaJ, an Escherichia coli Hsp40 protein composed of 376 amino acid residues, is a chaperone with thioldisulfide oxidoreductase activity. We present here for the first time a small angle x-ray scattering study of intact DnaJ and a truncated version, DnaJ (1-330), in solution. The molecular weight of DnaJ and DnaJ (1-330) determined by both small angle x-ray scattering and size-exclusion chromatography provide direct evidence that DnaJ is a homodimer and DnaJ (1-330) is a monomer. The restored models show that DnaJ is a distorted omega-shaped dimeric molecule with the C terminus of each subunit forming the central part of the omega, whereas DnaJ (1-330) exists as a monomer. This indicates that the deletion of the C-terminal 46 residues of DnaJ impairs the association sites, although it does not cause significant conformational changes. Biochemical studies reveal that DnaJ (1-330), while fully retaining its thiol-disulfide oxidoreductase activity, is structurally less stable, and its peptide binding capacity is severely impaired relative to that of the intact molecule. Together, our results reveal that the C-terminal (331-376) residues are directly involved in dimerization, and the dimeric structure of DnaJ is necessary for its chaperone activity but not required for the thiol-disulfide oxidoreductase activity.

Chromatography↗

PubMed2004

Unfolding kinetics of dimeric creatine kinase measured by stopped-flow small angle X-ray scattering.

The unfolding kinetics of creatine kinase (CK) in various concentrations of urea or guanidine hydrochloride (GuHCl) was investigated by small angle X-ray scattering (SAXS) using synchrotron radiation, and compared with the results obtained by stopped-flow circular dichroism and stopped-flow fluorescence. Using the three methods, the unfolding kinetics of CK fits well to a single exponential function with similar apparent rate constants, and the amplitude of the monophasic kinetics covers the entire range of the equilibrium values. The results suggest that the unfolding time-course measured by integrated SAXS intensity corresponds to the intramolecular loss of globular structure. The refolding kinetics of 8 M urea-denatured CK was monitored in a stopped-flow apparatus by following the spectroscopic changes, and the final state of folding was investigated by SAXS. A substantial part of the ellipticity is recovered within a burst phase, indicating that the secondary structure forms at an early stage in refolding. The R(g) value of the final folded state was 33.6 A when the folding buffer contained 20% glycerol, which is characteristic of native-like compactness and globularity.

Circular Dichroism↗

PubMed2002

Lysozyme viscoelastic matrices in tetramethylurea/water media: a small angle X-ray scattering study.

Semi-solid viscoelastic matrices produced out of lysozyme in organic/aqueous media [tetramethylurea (TMU)/water] were characterized by small angle X-ray scattering (SAXS). The scattering curves were modeled in their form and interference factors. Radii of gyration of scattering particles were found to undergo a dramatic increase from 14 A in water to approximately 44 A in the matrices. Average correlation distances d=155 A were consistently verified for the scattering particles in the matrices, irrespective of solvent composition (in the 0.6<or=w(TMU)<or=0.8 range), in contrast to what is observed in water (d=62 A). At w(TMU)=0.9, however, a slight increase in R(g) (to R(g)=49 A) leads to interdigitation with the apolar prevailing medium of the matrix leading to the loss of the interference effect. Low dimensionality derived from the modeling procedure could be taken to indicate mass fractal character of the unfolded species, although polydispersion of samples could also have some contribution to that result. Despite the very significant shape distortion of the unfolded protein forms in the matrices, they still retain considerable globular character, as indicated by the Kratky plots obtained. The morphological results obtained in this work are compatible with the dynamical behavior displayed by the systems.

Animals↗

PubMed1998

Determination of the fraction composition of blood lipoproteins by the small-angle X-ray scattering technique.

A new method for analyzing the fraction composition of blood lipoproteins (LP) was developed based on the small-angle X-ray scattering (SAXS) technique. The method allows quantitative determination of the contents of basic LP fractions (high-density LP, low-density LP, very low-density LP and their subfractions) in the blood plasma or serum. The results of LP analysis by the new method were compared with electron microscopy, ultracentrifugation and gel electrophoresis data. The results obtained by SAXS correlated with those obtained by traditional methods. The new method for the determination of the LP fraction composition in the blood is rapid (1-1.5 h), uses only one reagent (e.g., sucrose) and features a high accuracy and resolution up to LP subfractions. A total of 0.05 ml of the blood plasma or serum is required for an assay. The assays can be carried out in purified preparations or in the blood plasma or serum. The method developed can be used in clinical practice for diagnostics and in scientific research.

Chemistry, Clinical↗

PubMedDate not supplied

[Structure of Escherichia coli uracil DNA glycosylase and its complexes with nonhydrolyzable substrate analogues in solution observed by synchrotron small-angle X-ray scattering].

The structure of native and modified uracil DNA glycosylase from E. coli in solution was studied by synchrotron small-angle X-ray scattering. The modified enzyme (6His-uracyl DNA glycosylase) differs from the native one by the presence of an additional N-terminal 11-meric sequence amino acid residues including a block of six His residues. It was found that the conformations of these enzymes in solution at moderate ionic strength (60 mM NaCI) substantially differ in spite of minimal differences in the amino acid sequences and functional activity. The structure of native uracil DNA glycosylase in solution is close to that in crystal, showing a tendency for association. The interaction of this enzyme with nonhydrolyzable analogues of DNA ligands causes a partial dissociation of associates and a compactization of protein structure. At the same time, 6His-uracyl DNA glycosylase has a compact structure essentially different from the crystal one. A decrease in the ionic strength of solution results in a partial disruption of compact structure of the modified protein, without changes in its functional activity.

Escherichia coli↗

PubMed1986

Solution structure of halophilic malate dehydrogenase from small-angle neutron and X-ray scattering and ultracentrifugation.

Data from small-angle X-ray and neutron scattering and ultracentrifugation experiments on solutions of malate dehydrogenase from Halobacterium maris mortui are analysed together to yield a model for the enzyme particle formed by the protein and its interactions with water and salt in the solvent. The halophilic enzyme is stable only in high concentrations of salt and the model has structural features that are absent from non-halophilic malate dehydrogenase. The complementarity of the information derived from the three experimental methods is discussed extensively and quantitatively. It derives from the fact that mass density (ultracentrifugation), electron density (X-rays) and neutron scattering density are independent of each other. Each method gives a different "view" of the same particle, and an analysis of the combined data provided thermodynamic and structural parameters with, apart from the chemical composition of the solutions, only one other assumption: a constant partial specific volume for water equal to 1.00 cm3 g-1. Both the insights gained by this novel approach and its limitations are carefully pointed out. In solvents between 1 M and 5 M-NaCl, the enzyme forms a particle of invariant volume, consisting of a protein dimer (87,000 g mol-1) with which are associated 0.87 g of water and 0.35 g of salt per gram of protein. The partial specific volume of the protein calculated from the combined experimental data is 0.753(+/- 0.030) cm3 g-1, in good agreement with the value calculated from the amino acid composition. The particle has a radius of gyration of 32 A and an equivalent Stokes radius of 43 A. By combining the data from the X-ray and neutron scattering studies, the radii of gyration of the protein moiety alone and of the associated water and salt distribution were calculated. They are 28 A and about 40 A, respectively. The large-angle scattering curves show that the shapes of the particle and of the protein moiety alone are similar. At very low resolution they can be approximated by an ellipsoid of axial ratio 1:1:0.6 (or 1:1:1.5). At higher resolution, it becomes apparent that the particle has a significantly larger interface with solvent than an homogeneous ellipsoid or globular protein. The model has a globular protein core similar to non-halophilic malate dehydrogenase, with about 20% of the protein extending loosely out of the core, forming the large interface with solvent. The main interactions with water and salt take place on this outer part.

Halobacterium↗

PubMed1980

The solution shapes of IgG3 immunoglobulin and its Fch and Fc fragments. A small-angle X-ray scattering study.

A homogeneous IgG3 protein and its corresponding Fch and Fc fragments have been studied in solution using the small-angle X-ray scattering method. The Fch and Fc fragments were produced by short digestion of IgG3 with papain and trypsin. The results indicate that the overall shape of the IgG3 molecule in solution can best be described as an elliptical cylinder with a total length of 29 nm and with a cross-section having the semiaxes 3.8 and 0.9 nm. Thus, the overall shape of IgG3 is considerably different from the Y-shape normally adopted for the IgG1 molecule. The analysis of the data obtained for the Fch and Fc fragments also yields elliptical cylinders with almost the same dimensions of the cross-section but with shorter total lengths, 11.4 and 6.7 nm, respectively. The molecular weights of the IgG3 protein and the Fch and Fc fragments were determined to be 1.8 x 10(5), 0.61 x 10(5), and 0.50 x 10(5), respectively.

Humans↗

PubMed2002

Conformational landscape of cytochrome c folding studied by microsecond-resolved small-angle x-ray scattering.

To investigate protein folding dynamics in terms of compactness, we developed a continuous-flow mixing device to make small-angle x-ray scattering measurements with the time resolution of 160 micros and characterized the radius of gyration (R(g)) of two folding intermediates of cytochrome c (cyt c). The early intermediate possesses approximately 20 A of R(g), which is smaller by approximately 4 A than that of the acid-unfolded state. The R(g) of the later intermediate is approximately 18 A, which is close to that of the molten globule state. Considering the alpha-helix content (f(H)) of the intermediates, we clarified the folding pathway of cyt c on the conformational landscape defined by R(g) and f(H). Cyt c folding proceeds with a collapse around a specific region of the protein followed by a cooperative acquisition of secondary structures and compactness.

Cytochromes↗

PubMed1999

Small-angle x-ray scattering study of kinetics of spinodal decomposition in N-isopropylacrylamide gels.

We present synchrotron-based time-resolved small-angle x-ray scattering (SAXS) measurements of spinodal decomposition in a covalently cross-linked N-isopropylacrylamide gel. The range of wave numbers examined is well beyond the position of the maximum in the structure factor S(q,t). The equilibrium structure factor is described by the sum of a Lorentzian and a Gaussian. Following a temperature jump into the two phase region, the scattered intensity increases with time and eventually saturates. For early times the linear Cahn-Hilliard-Cook (CHC) theory can be used to describe the time evolution of the scattered intensity. From this analysis we found that the growth rate R(q) is linearly dependent on q(2), in agreement with mean-field theoretical predictions. However the Onsager transport coefficient Lambda(q) approximately q(-4), which is stronger than the q dependence predicted by the mean-field theory. We found that the growth rate R(q)>0, even though the wave numbers q probed by SAXS are greater than sqrt[2]q(m) where q(m) is the position of the peak of S(q,t), also in agreement with the mean-field predictions for a deep quench. We have also examined the range of validity of the linear CHC theory, and found that its breakdown occurs earlier at higher wave numbers. At later times, a pinning of the structure was observed. The relaxation to a final, microphase-separated morphology is faster and occurs earlier at the highest wave numbers, which probe length scales comparable to the average distance between crosslinks.

Journal Article↗

PubMed1984

Study of the Zn-containing DD-carboxypeptidase of Streptomyces albus G by small-angle X-ray scattering in solution.

Study of the Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase of Streptomyces albus G by small-angle X-ray scattering in solution yielded the following molecular parameters: radius of gyration R = 1.82 +/- 0.05 nm; largest diameter D = 5.9 +/- 0.2 nm; relative molecular mass Mr = 17000 +/- 2000; volume V approximately equal to 35 +/- 2 nm3; degree of hydration: 0.25 +/- 0.02 g water/g protein. By reference to theoretical scattering curves of rigid triaxial homogeneous bodies, a model which fits all experimental data is an elliptical cylinder. Such a model is compatible with that observed in the crystal structure. At those high concentrations necessary to form inactive enzyme-ligand associations the non-competitive beta-lactam inhibitors, cephalothin and cephalosporin C, drastically altered the scattering behaviour of the protein.

Carboxypeptidases↗

PubMed2003

Further insights into calmodulin-myosin light chain kinase interaction from solution scattering and shape restoration.

We have gained new insight into the interactions between the second-messenger protein calmodulin (CaM) and myosin light chain kinase from skeletal muscle (skMLCK) using small-angle solution scattering and shape restoration. Specifically, we explored the nature of a 2Ca(2+)-CaM-skMLCK complex and compared it to a 4Ca(2+)-CaM-skMLCK complex under the same conditions. The 2Ca(2+) complex has been proposed to be physiologically relevant. To aid in the interpretation of the data, we developed a shape restoration approach, implemented in GA_STRUCT, that combines many of the best features of other available methods into a single, automated package. Importantly, GA_STRUCT explicitly addresses the problem of the existence of multiple solutions to the inverse scattering problem and produces a consensus envelope from a set of shapes that fit the input intensity. Small-angle scattering intensity profiles measured or calculated from known structures were used to test GA_STRUCT, which was then used to generate low-resolution models for three complexes: 2Ca(2+)-CaM-skMLCK, 4Ca(2+)-CaM-skMLCK, and 4Ca(2+)-CaM-skMLCK with a bound substrate. These models were used in conjunction with high-resolution structures of the protein components to better understand the interactions among them. In the case of the 2Ca(2+)-CaM-skMLCK complex, the consensus envelope is consistent with CaM in a fully collapsed state with its two globular lobes in close contact with each other while the catalytic cleft of the kinase is open. The consensus envelope for the 4Ca(2+)-CaM-skMLCK complex indicates that the collapsed CaM has swung further away from the open catalytic cleft of the skMLCK than in the 2Ca(2+) complex, and further that substrate binding to this complex results in closure of the kinase catalytic cleft, in agreement with previous neutron scattering results. These results indicate that activation of MLCK by CaM can only occur once CaM is fully translocated away from the catalytic cleft, which is presumably linked to full release of the pseudo-substrate/inhibitory sequence. Our scattering data indicate that this step is completed only when all four calcium binding sites are loaded.

Amino Acid Sequence↗

PubMed2004

Comparison in fractal dimension between those obtained from structure factor and viscoelasticity of gel networks of 1,3:2,4-bis-O-(p-methylbenzylidene)-D-sorbitol in polystyrene melt at gel point.

We investigated time evolution of shear moduli in the physical gelation process of 1,3:2,4-bis-O-(p-methylbenzylidene)-D-sorbitol in polystyrene melt. At the gel point, storage and loss shear moduli, G' and G", were described by the power law of frequency omega, G' approximately G" approximately omegan, with the critical exponent n being nearly equal to 2/3, in agreement with the value predicted by the percolation theory. We also investigated the structure factor over two decades in length scale at gel point by using ultra-small-angle X-ray scattering, and small-angle X-ray scattering. We found the power-law behavior in low-q region, indicating that the gel network forms the self-similar structure with mass-fractal dimension. Comparison between the exponent of mass-fractal dimension from structure factor and that from viscoelasticity indicates that hydrodynamic interactions are completely screened out and the excluded volume effects are dominant in the gel. The gel strength was found to increase with the decrease in the lower limit length scale of fractality.

Benzylidene Compounds↗

PubMed1979

Neutron scattering on nuclei.

Very small angle neutron scattering studies have been made on intact nuclei under a variety of solution conditions. Scattering maxima are observed at 30 to 40 nm and at 18 nm in most environments. Although the spacing, intensity and presence of the maximum near 40 nm varies considerably with environment the 18 nm is rather constant. The 30 to 40 nm maximum appears to be best interpreted by the presence of 35 to 50 nm diameter fibers in nuclei. An important result is that no scattering maximum was observed near 11 nm, suggesting that a tightly super coiled nucleofilament with such a pitch is not present.

Animals↗

PubMed1997

Unfolding of dimeric creatine kinase in urea and guanidine hydrochloride as measured using small angle X-ray scattering with synchrotron radiation.

The denaturation of dimeric creatine kinase (CK) induced by urea and guanidine hydrochloride (GuHCl) has been studied by small angle X-ray scattering (SAXS), which is a direct way to measure the changes in the overall dimensions of a protein molecule. The radii of gyration (Rg) of CK are 29+/-0.4 angstroms in the native state and 46+/-1.5 angstroms in the unfolded state in either 8 M urea or 3 M GuHCl. The transition curves of urea denaturation derived from the Rg values and the zero angle intensity (I(0)) are similar to that from intrinsic fluorescence, indicating that the changes in the molecular shape, the tertiary structure and the dissociation of the subunits proceed simultaneously. In the case of GuHCl-induced denaturation, the dramatic increases both in Rg and in I(0) in 0.3-0.5 M GuHCl suggest clearly that soluble aggregates form at low GuHCl concentrations. The aggregates dissociate and the molecule unfolds at higher GuHCl concentrations. The results suggest that the mechanisms of CK denaturation in urea and in GuHCl are somewhat different and the intermediate in GuHCl denaturation can much more easily form soluble aggregates.

Animals↗

PubMed1999

Small angle X-ray scattering of wheat seed-storage proteins: alpha-, gamma- and omega-gliadins and the high molecular weight (HMW) subunits of glutenin.

Small angle X-ray scattering in solution was performed on seed-storage proteins from wheat. Three different groups of gliadins (alpha-, gamma- and omega-) and a high molecular weight (HMW) subunit of glutenin (1Bx20) were studied to determine molecular size parameters. All the gliadins could be modelled as prolate ellipsoids with extended conformations. The HMW subunit existed as a highly extended rod-like particle in solution with a length of about 69 nm and a diameter of about 6.4 nm. Specific aggregation effects were observed which may reflect mechanisms of self-assembly that contribute to the unique viscoelastic properties of wheat dough.

Gliadin↗

PubMed1999

Transient dimer in the refolding kinetics of cytochrome c characterized by small-angle X-ray scattering.

The equilibrium unfolding and the kinetic refolding of cytochrome c (Cyt c) in the presence of imidazole were studied with small-angle X-ray scattering (SAXS). The equilibrium unfolding experiments showed the radius of gyration, R(g), of native Cyt c to swell approximately 1 A with the addition of imidazole. The thermodynamic parameter m also reflects an expansion of the protein as its lower value demonstrates an increase in solvent-accessible surface area over that of native Cyt c in the absence of imidazole. Refolding was studied in the presence of imidazole as it prevents misligated intermediate states from forming during the refolding process, simplifying the kinetics, and making them easier to resolve. Time-resolved decreases in the forward scattering amplitude, I(0), demonstrated the transient formation of an aggregated intermediate. Final protein and denaturant concentrations were varied in the refolding kinetics, and the singular value decomposition (SVD) method was employed to characterize the associated state. This state was determined to be a dimer, with properties consistent with a molten globule.

Animals↗

PubMed2006

Rupture and regeneration of colloidal crystals as studied by two-dimensional ultra-small-angle X-ray scattering.

The structure of colloidal crystals of silica particles in water was studied by using the two-dimensional (2D) ultra-small-angle X-ray scattering (USAXS) technique. By violent shaking of the dispersion, large (body-centered cubic, bcc) crystals were broken into microcrystals while the lattice structure and lattice constant were preserved. The 2D-USAXS profiles revealed that the [111] direction of bcc microcrystals was parallel to the capillary axis and their orientational distribution with respect to the capillary axis was random. While a prepeak was observed in the one-dimensional USAXS measurements, no such peak was detected by the 2D-USAXS technique. The prepeak was concluded to be due to {110} being rotated by 54.7 degrees (the angle between [001] and [111]) from the capillary axis. The diffraction from the plane was out of the horizontal plane and was observed at a lower angle as a prepeak by detector scanning in the horizontal direction.

Journal Article↗

PubMed2006

Bone nanostructure near titanium and porous tantalum implants studied by scanning small angle x-ray scattering.

Bone sections including either titanium or porous tantalum implant devices used for interbody spinal fusion were investigated with position-resolved small angle X-ray scattering (sSAXS). The samples were obtained from six-month-old pigs that had undergone surgery three months prior to sacrifice. The aim of the study was to explore the possibility of using sSAXS to obtain information about thickness, orientation and shape/arrangement of the mineral crystals in bone near the implant surfaces. Detailed sSAXS scans were carried out in two different regions of bone adjacent to the implant in each of the implant samples. In the implant vicinity the mineral crystals tended to be aligned with the surface of the implants. The mean crystal thickness was between 2.1 and 3.0 nm. The mineral crystal thickness increased linearly with distance from the implant in both regions of the porous tantalum implant and in one of the regions in the titanium sample. In the second region of the titanium sample the thickest mineral crystals were found close to the implant surface. The observed differences in mineral thickness with distance from the implant surfaces might be explained by differences in mechanical load induced by the implant material and the geometrical design of the implant. The study shows that sSAXS is a powerful tool to characterize the nanostructure of bone near implant surfaces.

Humans↗