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PubMed2000

Polydispersity during the Formation and Growth of the Stöber Silica Particles from Small-Angle X-Ray Scattering Measurements.

The early stages of formation of Stöber silica particles have been investigated in situ during the hydrolysis and condensation of tetraethylorthosilicate under base-ammonia conditions in different alcoholic solvents. Time-resolved ultra-small-angle X-ray scattering by the entities produced in the solutions is used for structural characterization and monitoring of the growth kinetics of the particles. Our primary focus is to assess the polydispersity of the formed colloidal particles and its evolution as a function of time. We first applied a maximum entropy analysis of the scattering data to determine the size distribution and the time evolution of the size distribution of the colloidal particles. Second, we extended the cumulant method to analyze our earlier small-angle X-ray scattering data (H. Boukari, J. S. Lin, and M. T. Harris, J. Colloid Interface Sci. 194, 311, 1997; Chem. Mater. 9, 2376, 1997) and search for the presence of a distribution of fractal particles. The maximum entropy analysis indicates that there is a continuous nucleation of particles during the synthesis, and that this takes place within a relatively narrow size distribution. The cumulant analysis shows that, except at later times, the data are not adequate to confirm conclusively the presence of a distribution of fractal dimension at any time during the experiment. We discuss the impact of these results on growth kinetic models proposed for this system. Copyright 2000 Academic Press.

Journal Article↗

PubMed2001

Pressure-jump small-angle x-ray scattering detected kinetics of staphylococcal nuclease folding.

The kinetics of chain disruption and collapse of staphylococcal nuclease after positive or negative pressure jumps was monitored by real-time small-angle x-ray scattering under pressure. We used this method to probe the overall conformation of the protein by measuring its radius of gyration and pair-distance-distribution function p(r) which are sensitive to the spatial extent and shape of the particle. At all pressures and temperatures tested, the relaxation profiles were well described by a single exponential function. No fast collapse was observed, indicating that the rate limiting step for chain collapse is the same as that for secondary and tertiary structure formation. Whereas refolding at low pressures occurred in a few seconds, at high pressures the relaxation was quite slow, approximately 1 h, due to a large positive activation volume for the rate-limiting step for chain collapse. A large increase in the system volume upon folding implies significant dehydration of the transition state and a high degree of similarity in terms of the packing density between the native and transition states in this system. This study of the time-dependence of the tertiary structure in pressure-induced folding/unfolding reactions demonstrates that novel information about the nature of protein folding transitions and transition states can be obtained from a combination of small-angle x-ray scattering using high intensity synchrotron radiation with the high pressure perturbation technique.

Kinetics↗

PubMed1988

Small angle X-ray scattering study on bovine porphobilinogen synthase (5-aminolaevulinate dehydratase).

The quaternary structure of the native (zinc) porphobilinogen synthase (5-amino-laevulinate dehydratase) from bovine liver and its lead-substituted derivative is studied in solution by small angle X-ray scattering. In spite of the profound inhibitory effect of lead ions in the enzyme they do not produce a change in the quaternary structure detectable by small angle X-ray scattering. The most important molecular parameters of the native enzyme were found to be: radius of gyration Rg = 4.04 +/- 0.04 nm and maximum dimension Dmax = 12.0 +/- 0.5 nm. The corresponding values for the lead derivative are: Rg = 4.26 +/- 0.1 nm and Dmax = 12.5 +/- 0.5 nm. The quaternary structure of the enzyme in solution is described by a model, which fits the experimental scattering and distance distribution function.

Animals↗

PubMed1988

Application of the small-angle X-ray scattering technique for the study of equilibrium enzyme-substrate interactions of phenylalanyl-tRNA synthetase from E. coli with tRNAPhe.

The small-angle X-ray scattering technique (SAXS) is proposed for the investigation of equilibrium macromolecular interactions of the enzyme-substrate type in solution. Experimental procedures and methods of analysing 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 tRNAPhe with phenylalanyl-tRNA synthetase have been determined and demonstrate negative cooperativity for binding of the two tRNAPhe molecules. The structural parameters (Rg, Rc, semi-axes) have been determined for free phenylalanyl-tRNA synthetase and tRNAPhe from E. coli MRE-600 and of enzyme complexes possessing one and two tRNAPhe molecules, indicating structural rearrangements of the enzyme in the interaction with tRNAPhe.

Amino Acyl-tRNA Synthetases↗

PubMed2006

Gelatinization of starch in excess water: beyond the melting of lamellar crystallites. A combined wide- and small-angle X-ray scattering study.

The gelatinization of waxy rice, regular rice, and potato starch suspensions (66% w/w moisture) was investigated by real-time small-angle X-ray scattering (SAXS) and wide-angle X-ray diffraction (WAXD) during heating and by fast ramp differential scanning calorimetry (DSC). The high-angle tail of the SAXS patterns suggested the transition from surface to mass fractal structures in the DSC gelatinization range. Amylose plays a major role in determining the dimensions of the self-similar structures that develop during this process as the characteristic power-law scattering behavior extends to lower scattering angles for regular than for waxy starches. Crystallinity of A-type starches is lost in the temperature region roughly corresponding to the DSC gelatinization range. At the end of the gelatinization endotherm, the B-type potato starch showed residual crystallinity (WAXD), while SAXS-patterns exhibited features of remaining lamellar stacks. Results indicate that the melting of amylopectin crystallites during gelatinization is accompanied by the (exothermic) formation of amorphous networks.

Amylose↗

PubMed2006

Wavelet-based feature extraction applied to small-angle x-ray scattering patterns from breast tissue: a tool for differentiating between tissue types.

This paper reports on the application of wavelet decomposition to small-angle x-ray scattering (SAXS) patterns from human breast tissue produced by a synchrotron source. The pixel intensities of SAXS patterns of normal, benign and malignant tissue types were transformed into wavelet coefficients. Statistical analysis found significant differences between the wavelet coefficients describing the patterns produced by different tissue types. These differences were then correlated with position in the image and have been linked to the supra-molecular structural changes that occur in breast tissue in the presence of disease. Specifically, results indicate that there are significant differences between healthy and diseased tissues in the wavelet coefficients that describe the peaks produced by the axial d-spacing of collagen. These differences suggest that a useful classification tool could be based upon the spectral information within the axial peaks.

Algorithms↗

PubMed1993

Structural change of jack bean urease induced by addition of surfactants studied with synchrotron-radiation small-angle X-ray scattering.

Both the quaternary and subunit structures of jack bean urease in solutions with ionic and nonionic surfactants have been studied by small-angle X-ray scattering using a synchrotron-radiation source. The effects of those surfactants on the enzyme activity of urease have also been investigated in the same kind of solvent systems as those used for the scattering experiments. The present results show that the quaternary structure of urease in solution is fairly elongate and that by the relatively minor binding of SDS (SDS/protein = 0.23/1) the native urease molecule is dissociated into six identical subunits with nearly spherical structures. In addition the enzyme activity of urease was mostly retained under every solvent condition investigated, indicating that the subunit found in the present scattering experiments is the fundamental monomeric unit for both the quaternary-structure formation and enzyme function of urease.

Fabaceae↗

PubMed1997

Small-angle HeNe laser light scatter and the compressive modulus of articular cartilage.

Light scattering is a widely used technique for probing the microarchitecture and interactions of biological materials and solutions. In this paper, we describe the use of this method in the study of articular cartilage. The experiments presented utilize small-angle static scattering of HeNe laser light (632.8 nm) from 40 microns thick samples of cartilage taken from the superficial zone of baboon femoral condyle. The specimens were taken from a total of 26 sites in eight animals of various ages. In addition to measuring the dependence of the intensity of scattered light on scatter angle, we performed mechanical testing at the test sites using creep-indentation techniques. The results from the optical and mechanical experiments were compared, and a significant correlation was noted between the average scatter angle and the compressive aggregate modulus. In addition, it was noted that the cartilage of skeletally immature animals had a smaller aggregate modulus and scattered to a higher average angle than the cartilage of skeletally mature animals. A quantitative theory was developed to explain the relation, between mechanical and optical properties in terms of the degree of order in the spatial arrangement of the collagen fibers in cartilage.

Age Factors↗

PubMed1996

The methanol-induced globular and expanded denatured states of cytochrome c: a study by CD fluorescence, NMR and small-angle X-ray scattering.

Methanol-induced conformational transitions of cytochrome c(cyt c) at acidic pH values were investigated with a combined use of far and near-UV CD, fluorescence, NMR spectroscopy and small-angle X-ray scattering. At pH 3.0 and 25 degrees C, two methanol-induced non-native states were characterized. First, addition of methanol up to 25% (v/v) induced a compact denatured conformer (I(M)). Further addition of methanol transformed this I(M) state into the expanded and highly helical denatured state (H). The existence of the I(M) state was shown by the discrepancy in transition curves obtained from the ellipticity at 222 nm, the ellipticity at 282 nm, the tryptophan fluorescence monitored at 350 nm and the native peak intensity of the (1)H NMR spectrum. These CD, fluorescence and NMR results showed that the I(M) state has no specific tertiary structure but has a secondary structural content and tryptophan environment similar to those in the native state. The radius of gyration of the I(M) state, 17.7 angstroms, obtained from the Guinier plot of the small-angle X-ray scattering data was significantly smaller than that of the acid-denatured state (30.1 angstroms) and was closer to that of the native state (14.6 angstroms), showing that the I(M) state is compact. The Kratky plot for the I(M) state exhibited a bell-shaped profile, indicating a globular conformation. These structural features indicate that the structure of the I(M) state is quite similar to that of the anion-induced molten globule state of this protein. Furthermore the alcohol-denatured state (H) of cyt C in 60% (v/v) methanol was structurally characterized. Though the H state had a helical content much higher than the native state monitored by far-UV CD spectroscopy, the radius of gyration, 31.7 angstroms, was similar to that of the acid-denatured state, showing that this H state is an expanded denatured state. The Kratky plot for the H state did not show a clear peak, indicating a chain-like conformation. Thus we conclude that the H state has an expanded and chain-like conformation with a high helical content. Finally, we constructed a phase diagram of cyt c involving the native, I(M), acid-denatured and H states against pH and the methanol concentration. The result indicates that the I(M) state is found in the pH range from 2.5 to at least 4.5 with a pH-dependent optimum methanol concentration of 10 to 40%.

Circular Dichroism↗

PubMed1977

[Small-angle X-ray-scattering investigation and structural-model study of the fatty-acid synthetase from pig liver (author's transl)].

The structure of the fatty acid synthetase from pig liver was studied on models based upon structural and functional properties selected from pertinent results available from numerous investigations carried out with fatty acid synthetases from this and other sources. When comparing small-angle X-ray-scattering curves calculated with these models and curves obtained from small-angle X-ray-scattering experiments carried out with the pig-liver enzyme, we tried to select a model which would lead to an acceptable correlation between the calculated and the experimental curves and at the same time fulfil the known structural and functional requirements. The comparison of the curves was started with a model of low complexity. The observed discrepancy, together with arguments from the structural and the functional properties, helped decide which is the next most reasonable model to be considered. This procedure was repeated for five models of increasing complexity. In the model which led to the best fit the multienzyme complex is composed of two halves in an assymetric conformation including hollow spaces. This highly anisotropic model would imply that the two halves change their conformation each time a synthetic cycle is completed and that the growing fatty acid is handed over from one half to the other.

Animals↗

PubMed2003

Quaternary structure of alpha-crustacyanin from lobster as seen by small-angle X-ray scattering.

The structure of alpha-crustacyanin, the blue carotenoprotein of lobster (Homarus gammarus) carapace, has been investigated for the first time using small-angle X-ray scattering. In this paper, we have determined the dimensions of this protein composed of eight heterodimeric subunits of beta-crustacyanin. Analysis of the scattering spectra and estimation of the shape of alpha-crustacyanin show that the protein fits into a cylinder with an axial length of 238 A and a radius of 47.5 A, in which the eight beta-crustacyanin molecules are probably arranged in a helical manner.

Animals↗

PubMed2004

Structure of star-burst dendrimers: a comparison between small angle x-ray scattering and computer simulation results.

We investigated the generation dependent shape and internal structure of star-burst dendrimers under good solvent conditions using small angle x-ray scattering and molecular modeling. Measurements have been performed on poly(amidoamine) dendrimers with generations ranging from g=0 up to g=8 at low concentrations in methanol. We described the static form factor P(q) by a model taking into account the compact, globular shape as well as the loose, polymeric character of dendrimers. Monomer distributions within dendrimers are of special interest for potential applications and have been characterized by the pair correlation function gamma(r), as well as by the monomer and end-group density profile, rho(r) and rho(e)(r), respectively. Monomer density profiles and gamma(r) can be derived from P(q) by modeling and via a model independent approach using the inverse Fourier transformation algorithm first introduced by Glatter. Experimental results are compared with computer simulations performed for single dendrimers of various generations using the cooperative motion algorithm. The simulation gives direct access to gamma(r) and rho(r), allows an independent determination of P(q), and yields in addition to the scattering experiment information about the distribution of the end groups. Excellent qualitative agreement between experiment and simulation has been found.

Journal Article↗

PubMed2002

Millisecond-range time-resolved small-angle x-ray scattering studies of micellar transformations.

The transformation of mixtures of cationic and anionic micelles to vesicles has been studied by time-resolved small-angle x-ray scattering (SAXS). Equimolar amounts of ionic surfactant solutions, the anionic TexaponN70-H and the cationic TTAOH, were mixed by a stopped-flow device. Time-resolved SAXS patterns reveal that within the mixing time (<10 ms) mixed micelles are formed. These globular micelles dissolve within about 400-1000 ms and form monodisperse unilamellar vesicles in a much slower process of 5-100 s duration.

Micelles↗

PubMed1977

Studies by small-angle X-ray scattering of the quaternary structure of the beta-haemocyanin of Helix pomatia.

Helix pomatia beta-haemocyanin was studied in solution by small-angle X-ray scattering. The following molecular parameters were determined: molecular weight = 9.02 X 10(6), volume = 14000 nm3, radius of gyration = 18.4 nm, radius of the spherical subunits = 2.5 +/- 0.2 nm. With these data, and with information of dissociation products described in a former paper, a model of the molecule was built whose theoretical scattering curve showed good agreement with the experimental one. The model consists of 160 spherical subunits of a radius of 2.5 nm; 12 rings each built up of 10 spheres form the outer wall of a hollow cylinder; 20 subunits are situated at the inner side of each end.

Animals↗

PubMed1982

The interaction of calf thymus DNA with mercuric acetate and 3,6-bis-(acetatomercurimethyl)-dioxane. Small-angle X-ray scattering and viscosity studies.

The binding of Hg2+ and 3,6-bis-(acetatomercurimethyl)-dioxane (BAMD) to sonicated calf thymus DNA was studied by small-angle X-ray scattering and viscosity measurements. The scattering experiments with DNA complexed by different amounts of mercurials (for Hg2+ rb=0-0.79, for BAMD rb=0-0.86 mol of mercurial bound per mol of base pairs) established that the rod-like character of the DNA molecules is maintained up to high binding ratios. They revealed further a steady decrease of the cross-section radius of gyration Rc for the DNA X Hg2+ complex and a similar decrease of Rc for the DNA X BAMD complex up to Rb=0.35. This behaviour is certainly caused by the incorporation of both mercurials near the axis of the DNA helix. Binding of BAMD at rb greater than 0.35 led to an increase of Rc which behaviour obviously reflects the location of mercury atoms at large distances from the axis, possibly on the surface of the helix. The increase of the mass per unit length Mc upon binding of the mercurials was found to be much higher than expected. This finding established that the length of the DNA helix decreases by 0.10 +/- 0.01 nm per bound mercurial at low binding ratios (i.e. up to rb=1/3 for BAMD, up to possibly rb=0.5 for Hg2+). A similar conclusion was also drawn from the observed decrease of intrinsic viscosity [n] with increasing rb. The analysis of Mc at high binding ratios suggests that every BAMD molecule bound beyond rb=1/3 decreases the length of the DNA by 0.21 +/- 0.05 nm whereas Hg2+ when bound beyond rb=0.5 causes no change of the length.

Animals↗

PubMed1997

Three-dimensional structure of maize alpha-zein proteins studied by small-angle X-ray scattering.

alpha-zeins of maize (Zea mays) that are storage proteins contain nine or ten tandem repeats comprising of about 20 amino acids. Small-angle X-ray scattering (SAXS) of alpha-zeins was measured in 70% (v/v) aqueous ethanol containing beta-mercaptoethanol or without reagent in a protein concentration range of 2.0 to 40.0 mg/ml. The overall radius of gyration of whole particles, Rg, and the corresponding radius of gyration of the cross-section, Rc, of reduced alpha-zeins are 4.00 +/- 0.03 nm and 1.39 +/- 0.05 nm, respectively, in the 70% (v/v) aqueous ethanol containing 2% (v/v) beta-mercaptoethanol. Analyses using the Rg and Rc values indicate that reduced alpha-zeins exist as asymmetric particles with the length of about 13 nm in the solution. A structural model is developed under assumption that each of tandem repeats units forms single alpha-helix and they are joined by glutamine-rich 'turns' or loops, as employed by Argos et al., [Argos, O., Pedersen, K., Marks, M.D. and Larkins, B.A. (1982) J. Biol. Chem. 257, 9984-9990] and Garratt et al. [Garratt, R., Oliva, G., Caracelli, I., Leite, A. and Arruda, P. (1993) Proteins Struc. Func. Genet. 15, 88-99], and that the longest dimension of 13 nm comes from linear stacking of the anti-parallel helices of tandem repeat in the direction perpendicular to the helical axis. The resultant model is presented by an elongated prism-like shape with an approximate axial ratio of 6:1.

Mathematics↗

PubMed1996

Conformational characterization of DnaK and its complexes by small-angle X-ray scattering.

DnaK, a member of the 70 kDa heat shock protein (hsp70) family, and its complexes with substrate proteins and nucleotides were characterized by small-angle X-ray scattering (SAXS) and size-exclusion chromatography (SEC) techniques. The SAXS data indicated that DnaK has a dumbbell-shaped structure with a maximum dimension (dmax) of 112 angstrom, which is consistent with the reported two major functional domains [Chappell et al. (1987) J. Biol. Chem. 268, 12730-12735; Flaherty et al. (1990) Nature 346, 623-628]. The data were best fit by a model in which the two domains either are connected by a short hinge region or are just in contact with each other. The radius of gyration (Rg) of DnaK was determined as 37.5 +/- 1.0 angstrom in the absence of nucleotide. Binding of ATP induces a conformational change in DnaK as reflected by the changes in its P(r) function and Kratky plot, the increases (1-2 angstrom) in both its radius of gyration (Rg) and its Stokes radius (Rs), and the increase in its dmax (5-10 angstrom ). SAXS and SEC-HPLC results indicate that the association state of DnaK is very sensitive to the buffer concentration and the presence of substrates, as well as the protein concentration. At high buffer and protein concentrations, DnaK dimerizes, resulting in an increase in its apparent Rg and dmax values. The addition of substrate (unfolded protein or ATP) results in a return to the Rg value of monomeric DnaK, due to the dissociation of DnaK multimers induced by the substrate binding and resultant conformational changes. The DnaK-substrate protein complex gives a smaller Rg than expected, suggesting that the substrate protein binds to a cavity or cleft on DnaK rather than the exterior of the chaperone. The Kratky plot of the Gdn.HCl-induced unfolding intermediate state of DnaK is consistent with a compact, molten globule-like conformation, as previously suggested based on CD, fluorescence, and SEC-HPLC results [Palleros et al. (I 993) Biochemistry 32, 4314-4321].

Bacterial Proteins↗

PubMed2000

Further evidence of spinodal decomposition during the induction period of polymer crystallization: time-resolved small-angle x-ray scattering prior to crystallization of poly(ethylene naphthalate)

Aiming to clarify spinodal decomposition of polymers in the induction period of crystallization, time-resolved small-angle x-ray scattering measurements have been made in situ for poly(ethylene naphthalate) while it was crystallized from the glass, or in the case of the so-called glass crystallization. It is confirmed for this polymer that in the very beginning of the induction period a scattering peak appears at around 0.03 A (-1) in scattering vector q, which corresponds to a characteristic wavelength of 200 A in density fluctuations, and grows with time. Time evolution of this scattering peak is described by the kinetics of the spinodal decomposition as previously reported for the glass crystallization of poly(ethylene terephthalate).

Journal Article↗