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PubMed1991

Nucleation and growth of mineral crystals in bone studied by small-angle X-ray scattering.

The mechanism of calcification in bone and related tissues is a matter of current interest. The mean size and the arrangement of the mineral crystals are important parameters difficult to obtain by electron microscopy. Furthermore, most studies have been carried out on poorly calcified model systems or chemically treated samples. In the work presented here, native bone was studied as a function of age by a quantitative small-angle X-ray scattering method (SAXS). Bone samples (calvariae and ulnae) from rats and mice were investigated. Measurements were performed on native bone immediately after dissection for samples up to 1 mm thick. The size, shape, and predominant orientation of the mineral crystals in bone were obtained for embryonal, young, and adult animals. The results indicate that the mineral nucleates as thin layers of calcium phosphate within the hole zone of the collagen fibrils. The mineral nuclei subsequently grow in thickness to about 3 nm, which corresponds to maximum space available in these holes.

Animals↗

PubMed2006

Investigation of the structure of cellulose in LiCl/DMAc solution and its gelation behavior by small-angle X-ray scattering measurements.

Cellulose gels were prepared from cellulose in lithium chloride/N,N-dimethylacetamide (LiCl/DMAc) solution. When the cellulose concentration in the solution is above the one at which cellulose molecules overlap, cellulose gels were formed. While the gel prepared by the addition of water was turbid, the one prepared by the ion exchange was colorless, transparent, and optically anisotropic. In order to explain this gelation behavior of cellulose, small-angle X-ray scattering (SAXS) measurements of the cellulose solutions and the gels were performed. The SAXS profiles of the cellulose solutions and the gels suggested that the large-scale fluctuation of the molecular chain density in the solution can be the origin of the molecular aggregates formed in the gel. Furthermore, the differences in the structure of the gels at the macroscopic and the molecular level were discussed in terms of the phase separation and the molecular association.

Acetamides↗

PubMed1983

Neutron scattering studies of nucleosome structure at low ionic strength.

Ionic strength studies using homogeneous preparations of chicken erythrocyte nucleosomes containing either 146 or 175 base pairs of DNA show a single unfolding transition at about 1.5 mM ionic strength as determined by small-angle neutron scattering. The transition seen by some investigators at between 2.9 and 7.5 mM ionic strength is not observed by small-angle neutron scattering in either type of nucleosome particle. The two contrasts measured (H2O and D2O) indicate that only small conformational changes occur in the protein core, but the DNA is partially unfolded below the transition point. Patterson inversion of the data and analysis of models indicate that the DNA in both types of particle is unwinding from the ends, leaving about one turn of supercoiled DNA bound to the histone core in approximately its normal (compact) conformation. The mechanism of unfolding appears to be similar for both types of particles and in both cases occurs at the same ionic strength. The unfolding observed for nucleosomes in this study is in definite disagreement with extended superhelical models for the DNA and also disagrees with models incorporating an unfolded histone core.

Animals↗

PubMed2006

Small-angle X-ray scattering reveals the solution structure of a bacteriophytochrome in the catalytically active Pr state.

Phytochromes are light-sensing macromolecules that are part of a two component phosphorelay system controlling gene expression. Photoconversion between the Pr and Pfr forms facilitates autophosphorylation of a histidine in the dimerization domain (DHp). We report the low-resolution structure of a bacteriophytochrome (Bph) in the catalytic (CA) Pr form in solution determined by small-angle X-ray scattering (SAXS). Ab initio modeling reveals, for the first time, the domain organization in a typical bacteriophytochrome, comprising an chromophore binding and phytochrome (PHY) N terminal domain followed by a C terminal histidine kinase domain. Homologous high-resolution structures of the light-sensing chromophore binding domain (CBD) and the cytoplasmic part of a histidine kinase sensor allows us to model 75% of the structure with the remainder comprising the phytochrome domain which has no 3D representative in the structural database. The SAXS data reveal a dimeric Y shaped macromolecule and the relative positions of the chromophores (biliverdin), autophosphorylating histidine residues and the ATP molecules in the kinase domain. SAXS data were collected from a sample in the autophosphorylating Pr form and reveal alternate conformational states for the kinase domain that can be modeled in an open (no-catalytic) and closed (catalytic) state. This model suggests how light-induced signal transduction can stimulate autophosphorylation followed by phosphotransfer to a response regulator (RR) in the two-component system.

Adenosine Triphosphate↗

PubMed1989

Structure of tyrocidine micelles in isotropic aqueous solution.

Aqueous solutions of tyrocidine B, iodoacetyltyrocidine B, and diiodotyrocidine B in 40% H2O:60% ethanol (w/w) were investigated by analytical ultracentrifugation, light scattering, and small-angle X-ray scattering techniques. A reasonable hydrodynamic description of the aggregates of molecular weight 28,600 is a rod with a length of 170 A and a diameter of 30 A; this description is consistent with the X-ray scattering data. Over a broad range of concentrations, inelastic light scattering measurements and small-angle X-ray scattering experiments provide the same hydrodynamic values (e.g., Stokes radii and frictional ratios). The positions of the iodines were resolved and found at a radius (R) of 16 A. So, the iodine-iodine distance across the cross section is 34 A, indicating that labeled tyrocidine B is not affected during the aggregational process.

Chemical Phenomena↗

PubMed2003

Structural stability and solution structure of chaperonin GroES heptamer studied by synchrotron small-angle X-ray scattering.

The GroES protein from Escherichia coli is a well-known member of the molecular chaperones. GroES consists of seven identical 10 kDa subunits, and forms a dome-like oligomeric structure. In order to obtain information on the structural stability and unfolding-refolding mechanism of GroES protein, especially at protein concentrations (0.4-1.2 mM GroES monomer) that would mimic heat stress conditions in vivo, we have performed synchrotron small-angle X-ray scattering (SAXS) experiments. Surprisingly, in spite of the high protein concentration, reversibility in the unfolding-refolding reaction was confirmed by SAXS experiments structurally. Although the unfolding-refolding reaction showed an apparent single transition with a Cm of 1.1 M guanidium hydrochloride, a more detailed analysis of this transition demonstrated that the unfolding mechanism could be best explained by a sequential three-state model, which consists of native heptamer, dissociated monomer, and unfolded monomer. Together with our previous result that GroES unfolded completely via a partially folded monomer according to a three-state model at low protein concentration (5 microM monomer), the unfolding-refolding mechanism of GroES protein could be explained uniformly by the three-state model from low to high protein concentrations. Furthermore, to clarify an ambiguity of the native GroES structure in solution, especially mobile loop structures, we have estimated a solution structure of GroES using SAXS profiles obtained from experiments and simulation analysis. The result suggested that the native structure of GroES in solution was very similar to that seen in GroES-GroEL complex determined by crystallography.

Chaperonin 10↗

PubMed1989

Solution structure of human plasma fibronectin as a function of NaCl concentration determined by small-angle X-ray scattering.

The structure of human plasma fibronectin in 50 mM Tris-HCl buffer, pH 7.4, containing varying concentrations of NaCl, has been investigated using the small-angle X-ray method. Below 0.3 M NaCl the overall structure of the molecule is disc-shaped; at 0 M NaCl the axial ratio of the disc is about 1:7 and between 0.1 M to 0.3 M it is slightly more asymmetric, with an axial ratio of 1:10. At about 0.3 M NaCl there is a reversible transition to a more open structure, and, from 0.3 M up to 1.1 M NaCl the small-angle X-ray data can be explained by models consisting of ensembles of flexible, non-overlapping, bead-chains generated by a Monte Carlo procedure. Within this concentration range there is a gradual increase in the stiffness of the chains, as well as a decrease in bead radius, which indicates that the molecule becomes more open when the NaCl concentration is increased. The transition to a more open structure is also demonstrated by the average radius of gyration which increases gradually from 8.26 nm at 0 M NaCl to 8.75 nm at physiological or near-physiological conditions, and up to 16.2 nm at 1.1 M NaCl.

Fibronectins↗

PubMedDate not supplied

Stained native collagen: interpretation of the small angle X-ray scattering and electron microscopic pictures in terms of the primary structure.

The average axial electron-density distribution of stained collagen fibers derived from X-ray small angle pattern, is shown to be substantially related to the projection of the polar amino acid residues onto the axis of the microfibril taking into consideration the staggering of neighbouring molecules. In order to arrive ultimately at a quantitative representation of the experimental data, an additional periodic fluctuation of the density in direction of the fibril axis is required. The necessity of this regular microphase structure for an understanding of known physical properties of collagen fibers will be indicated.

Amino Acid Sequence↗

PubMed1995

Interactions between liposomes and human stratum corneum in vitro: freeze fracture electron microscopical visualization and small angle X-ray scattering studies.

The interactions between three liposomal formulations and human stratum corneum were visualized using freeze fracture electron microscopy. A new replica cleaning method was introduced. Human stratum corneum was submerged for 48 h in liposome suspensions prepared from commercially available phospholipid mixtures. The size, lamellarity and lipid moieties of the liposomes were similar. The main difference between the three phospholipid formulations was the hydrophilicity of the headgroups. The composition dependence of the interactions between these vesicles and human stratum corneum was investigated. In essence, two types of interaction were observed: adsorption of the liposomes on to the outer surface of the stratum corneum, and ultrastructural changes in deeper layers of the stratum corneum caused by mixing of the liposomal constituents and the stratum corneum lipids. The electron microscopic observations were verified with small-angle X-ray scattering. It was found that liposomes composed of phospholipids containing relatively small hydrophilic headgroups showed a marked interaction with the skin lipids of human stratum corneum in vitro. The complexity of the phospholipid mixtures, however, made it very difficult to determine the exact effect each of these headgroups has on the interactions between these vesicles and human stratum corneum.

Adsorption↗

PubMed2005

Effects of confined geometry on phase-separated dextran/gelatine mixtures exposed to shear.

The effect of shear on aqueous phase-separated dextran/fish gelatine mixtures with a total concentration of 5 and 10% was studied in a confined geometry. It was measured as a function of composition, strain rate and gap size. This was done by using both small-angle light scattering and a shear cell combined with a confocal laser scanning microscope. At a total polymer concentration of 5%, small-angle light scattering results showed that up to 100 s(-1) the deformation of the domains increases with the strain rate. At strain rates less than 100 s(-1), the response of the system to strain is dominated by strain rate-dependent deformation. At a higher strain rate there might be balance between break-up and re-coalescence. At a total concentration of 10%, small effects of the gap size were found. In confined geometry, the coalescence rate was faster than expected from viscous hydrodynamic growth. The microscope images showed that the gelatine-enriched phase forms a wetting layer on the surface of the glass wall. The degree of wetting appears to increase with increasing the strain rate up to 60 s(-1) and decreases again at higher strain rates.

Journal Article↗

PubMed2004

Exploring the melting of a semirigid-chain polymer with temperature-resolved small-angle X-ray scattering.

The thermal behavior of semirigid semicrystalline polymers differs significantly from that of flexible-chain polymers. The origin of the differences is believed to lie in the higher energy expenditure associated with the formation of adjacent re-entry folds at the crystalline surface in the case of semirigid chains. The effect of constraints imposed by the interlamellar amorphous regions on the neighboring crystals was studied with temperature-resolved synchrotron radiation small-angle X-ray scattering (SAXS). The analysis of SAXS patterns with a generalized paracrystalline lamellar stack model indicates that melting of a semirigid-chain polymer is not a random process but that the crystals grown in the smallest amorphous gaps melt first. This suggests that the hitherto largely neglected geometrical confinement effects may play an important role in determining the thermodynamic stability of semirigid-chain polymer crystals.

Biophysics↗

PubMedDate not supplied

Small angle X-ray scattering of resistant starch type III.

Starch fraction, which is resistant to enzymatic digestion, is produced during retrogradation. This fraction, termed resistant starch type III (RSIII), has health benefits such as pre-biotic effects, improving lipid and cholesterol metabolism, and reducing the risk of colon cancer. The work presented in this paper is aimed at investigating the colloidal structure of native high amylose corn starch (HACS) and the RSIII polymorphs produced from it using small angle X-ray scattering. Experimental scattering curves were fitted with appropriate theoretical models such as the "modified lamellar model". Our results show that retrogradation at low temperature leads to formation of polymorph B with crystallinity much lower than that of the granular form, but the lamellas are arranged in long-range periodicity. Conversely, retrogradation at high temperature leads to formation of polymorphs A and V with no defined periodicity. The degree of crystallinity is very low, and the system is better described as a dilute particulate system.

Amylose↗

PubMed2004

Supported particle track etched polyimide membranes: a grazing incidence small-angle X-ray scattering study.

Particle track etched polyimide membranes on silicon substrates covered with a native oxide layer are investigated. Preparation steps similar to the common classical particle track etched membrane production, giving rise to free-standing membranes, are successfully applied to the supported membranes. Polyimide films are used as a starting material for a template preparation based on high energy ion irradiation. The film/membrane structure is probed at different length scales by grazing incidence small-angle X-ray scattering at each individual preparation step. In addition, characterization with atomic force microscopy, variable-angle spectroscopic ellipsometry, Fourier transform infrared transmission, and attenuated total reflection spectroscopy is performed. An amount of 6 +/- 1 vol % pores inside the polyimide film is detected. The pores are oriented perpendicular to the substrate surface and have a conical shape, yielding a slightly reduced pore size at the substrate/film interface.

Journal Article↗

PubMed2006

Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray scattering.

We study the structure of carboxylic acid terminated neutral poly(propyl ether imine) (PETIM) dendrimer from generations 1-6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation the structural properties such as radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by small angle x-ray scattering experiment on dendrimer of generations 2-4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as approximately Nx with the number of monomers. We find two distinct exponents depending on the generations, x=0.47 for G1-G3 and x=0.28 for G3-G6, which reveal their nonspace filling nature. In comparison with the amine terminated poly(amidoamine) (PAMAM) dendrimer, we find that Rg of Gth generation PETIM dendrimer is nearly equal to that of (G+1)th generation of PAMAM dendrimer as observed by Maiti et al. [Macromolecules 38, 979 (2005)]. We find substantial back folding of the outer subgenerations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules, suggesting the use of PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.

Journal Article↗

PubMed2006

The denaturation transition of DNA in mixed solvents.

The helix-to-coil denaturation transition in DNA has been investigated in mixed solvents at high concentration using ultraviolet light absorption spectroscopy and small-angle neutron scattering. Two solvents have been used: water and ethylene glycol. The "melting" transition temperature was found to be 94 degrees C for 4% mass fraction DNA/d-water and 38 degrees C for 4% mass fraction DNA/d-ethylene glycol. The DNA melting transition temperature was found to vary linearly with the solvent fraction in the mixed solvents case. Deuterated solvents (d-water and d-ethylene glycol) were used to enhance the small-angle neutron scattering signal and 0.1M NaCl (or 0.0058 g/g mass fraction) salt concentration was added to screen charge interactions in all cases. DNA structural information was obtained by small-angle neutron scattering, including a correlation length characteristic of the inter-distance between the hydrogen-containing (desoxyribose sugar-amine base) groups. This correlation length was found to increase from 8.5 to 12.3 A across the melting transition. Ethylene glycol and water mixed solvents were found to mix randomly in the solvation region in the helix phase, but nonideal solvent mixing was found in the melted coil phase. In the coil phase, solvent mixtures are more effective solvating agents than either of the individual solvents. Once melted, DNA coils behave like swollen water-soluble synthetic polymer chains.

Circular Dichroism↗

PubMed2005

Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit.

DNA gyrase is the topoisomerase uniquely able to actively introduce negative supercoils into DNA. Vital in all bacteria, but absent in humans, this enzyme is a successful target for antibacterial drugs. From biophysical experiments in solution, we report the low-resolution structure of the full-length A subunit (GyrA). Analytical ultracentrifugation shows that GyrA is dimeric, but nonglobular. Ab initio modeling from small-angle X-ray scattering allows us to retrieve the molecular envelope of GyrA and thereby the organization of its domains. The available crystallographic structure of the amino-terminal domain (GyrA59) forms a dimeric core, and two additional pear-shaped densities closely flank it in an unexpected position. Each accommodates very well a carboxyl-terminal domain (GyrA-CTD) built from a homologous crystallographic structure. The uniqueness of gyrase is due to the ability of the GyrA-CTDs to wrap DNA. Their position within the GyrA structure strongly suggests a large conformation change of the enzyme upon DNA binding.

Amino Acid Sequence↗

PubMed1991

Tertiary and quaternary structural differences between two genetic variants of bovine casein by small-angle X-ray scattering.

The casein complexes of bovine milk consist of four major protein fractions, alpha s1, alpha s2, beta, and kappa. Colloidal particles of casein (termed micelles) contain inorganic calcium and phosphate; they are very roughly spherical with an average radius of 650 A. Removal of Ca2+ leads to the formation of smaller protein aggregates (submicelles) with an average radius of 94 A. Two genetic variants, A and B, of the predominant fraction, alpha s1-casein, result in milks with markedly different physical properties, such as solubility and heat stability. To investigate the molecular basis for these differences, small-angle X-ray scattering was performed on the respective colloidal micelles and submicelles. Scattering curves for submicelles of both variants showed multiple Gaussian character; data for the B variant were previously interpreted in terms of two concentric regions of different electron density, i.e., a "compact" core and a relatively "loose" shell. For the submicelle of A, there was a third Gaussian, reflecting a negative contribution due to interparticle interference. Molecular parameters for submicelles of both A and B are in agreement with hydrodynamic data in the literature. Data for the micelles, for which scattering yields cross-sectional information, were fitted by a sum of three Gaussians for both variants; for these, the corresponding two lower radii of gyration represent the two concentric regions of the submicelles, while the third reflects the average packing of submicelles within the micellar cross section. Most of the molecular parameters obtained showed small but consistent differences between A and B, but for submicelles within the micelle several differences were particularly notable: A has a greater molecular weight for the "compact" region of the constituent submicelle (82,000 vs 60,000) and a much greater submicellar packing number (6:1 vs 3:1). Reasons for these and other differences are to be sought in sequence differences and in differences in calcium-binding sites and charge distribution.

Animals↗

PubMed2005

Structural insights into the beta-xylosidase from Trichoderma reesei obtained by synchrotron small-angle X-ray scattering and circular dichroism spectroscopy.

The enzyme beta-xylosidase from Trichoderma reesei, a member of glycosil hydrolase family 3 (GH3), is a glycoside hydrolase which acts at the glycosidic linkages of 1,4-beta-xylooligosaccharides and that also exhibits alpha-l-arabinofuranosidase activity on 4-nitrophenyl alpha-l-arabinofuranoside. In this work, we show that the enzyme forms monomers in solution and derive the low-resolution molecular envelope of the beta-xylosidase from small-angle X-ray scattering (SAXS) data using the ab initio simulated annealing algorithm. The radius of gyration and the maximum dimension of the beta-xylosidase are 30.3 +/- 0.2 and 90 +/- 5 A, respectively. In contrast to the fold of the only two structurally characterized members of GH3, the barley beta-d-glucan exohydrolase and beta-hexosaminidase from Vibrio cholerae, which have respectively two or one distinct domains, the shape of the beta-xylosidase indicates the presence of three distinct structural modules. Domain recognition algorithms were used to show that the C-terminal part of the amino acid sequence of the protein forms the third domain. Circular dichroism spectroscopy and secondary structure prediction programs demonstrate that this additional domain adopts a predominantly beta conformation.

Algorithms↗