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PubMed2006

Solution structure and dynamics of cartilage aggrecan.

We studied the structure and dynamics of porcine laryngeal aggrecan in solution using a range of noninvasive techniques: dynamic light scattering (DLS), small-angle neutron scattering (SANS), video particle tracking (VPT) microrheology, and diffusing wave spectroscopy (DWS). The data are analyzed within the framework of a combined static and dynamic scaling model, and evidence is found for reptation of the comb backbones with unentangled side-chain dynamics. Small-angle neutron scattering indicated standard polyelectrolyte scaling of the mesh size (xi) with concentration (c) in semidilute solutions for the whole aggrecan aggregate, xi = Ac(-0.47+/-0.04), with the prefactor (A) implying there is on average 60 nm between the aggrecan subunits along the backbone. VPT demonstrated large exponents for the power law dependence of the intrinsic viscosity (eta) on the polymer concentration in the semidilute concentration regime, eta approximately c(alpha); with alpha equal to 2.04 +/- 0.06 and 1.95 +/- 0.08 for the assembled and disassembled aggrecan aggregates, respectively. DWS at high frequencies (10(4)-10(5) Hz) gave evidence for internal Rouse modes of the aggrecan monomers, independent of the degree of self-assembly of the molecules.

Aggrecans↗

PubMed2005

Small-angle X-ray scattering and light scattering on lysozyme and sodium glycocholate micelles.

Small-angle X-ray scattering (SAXS) together with static (SLS) and dynamic light scattering (DLS) measurements were carried out on aqueous solutions of lysozyme (LY) and of the ionic biological detergent sodium glycocholate (NaGC). Apparent diffusion coefficients (D app), excess Rayleigh ratio, and SAXS spectra were measured for 0.1 M NaGC solutions at different ionic strengths (0.05-0.30 M NaCl). The same data were collected for LY in sodium acetate buffer 50 mM without and with 92 mM NaCl as a function of protein concentration (10-80 g L(-1)). A correlated analysis of SLS data and SAXS spectra was first tested on the LY samples and then extended to the interpretation of the NaGC data to infer information on particle structure and interaction potential. A hard-core (HC) interaction shell of uniform thickness, a screened Coulomb potential of the electric double layer (EDL) or the complete DLVO potential were alternatively used to represent the long-range tail of the interaction potential. Whenever an essentially repulsive tail is expected, all the representations give reasonable results, but the data analysis does not allow the discrimination between the oblate and the prolate symmetries of the NaGC aggregates. The DLVO model allows the interpretation of the data even when the attractive component determines the tail character. With this model an overall fit of the micelle data at all the NaCl concentrations was successfully performed by assuming a simple spherical symmetry of the micelles and invariant values of their ionization degree and Hamaker constant, thus considering just the screening effect of the added electrolyte. Whatever model is used, the results point out that the aggregates are quite hydrated (26-38 water molecules per monomer) and very slightly grow by increasing the NaCl concentration. When spherical symmetry is assumed the aggregate radii for all the samples fall in the range 15-16 A. From the SAXS and SLS, best fitting geometrical parameters, and interparticle structure factor, a D app value was calculated for each sample. An excellent consistence is achieved for LY results. On the contrary, calculated D app values systematically lower than the experimental values are always obtained for the NaGC micelles. Micelle polydispersity and internal dynamics seem to be the most probable reasons of the bad agreement.

Glycocholic Acid↗

PubMed1998

First performance assessment of the small-angle X-ray scattering beamline at ELETTRA.

The double-focusing high-flux wiggler beamline dedicated to small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS) at ELETTRA has gone into user operation recently. It has been designed specifically for time-resolved studies of non-crystalline and fibrous materials in the submillisecond time scale, and has been optimized for small-angle scattering measurements. An overview of the beamline status and of some representative results, highlighting the performance of the SAXS beamline, are given.

Journal Article↗

PubMed2003

Determination of asymmetric structure of ganglioside-DPPC mixed vesicle using SANS, SAXS, and DLS.

Functions of mammalian cell membrane microdomains being rich in glycosphingolipids, so-called rafts, are now one of the current hot topics in cell biology from the intimate relation to cell adhesion and signaling. However, little is known about the role of glycosphingolipids in the formation and stability of the domains. By the use of the inverse contrast variation method in small-angle neutron scattering (SANS), combined with small-angle x-ray scattering (SAXS) and dynamic light scattering (DLS), we have determined an asymmetric internal structure of the bilayer of the small unilamellar vesicle (SUV) of monosialoganglioside (G(M1))-dipalmitoylphosphatidylcholine (DPPC) mixture ([G(M1)]:[DPPC] = 0.1:1). A direct method using a shell-model fitting with a size distribution function describes consistently all experimental results of SANS, SAXS, and DLS. We have found that G(M1) molecules predominantly localize at SUV outer surface to form a highly hydrophilic layer which is dehydrated with the rise of temperature from 25 degrees C to 55 degrees C accompanied by the conformational change of the oligosaccharide chains. The average SUV size determined is approximately 200 A, which is comparable to the reported value 260 +/- 130 A of glycosphingolipids microdomains. The present results suggest that the preferential asymmetric distribution of gangliosides is essential to define the size and stability of the domains.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

How large is an alpha-helix? Studies of the radii of gyration of helical peptides by small-angle X-ray scattering and molecular dynamics.

Using synchrotron radiation and the small-angle X-ray scattering technique we have measured the radii of gyration of a series of alanine-based alpha-helix-forming peptides of the composition Ace-(AAKAA)(n)-GY-NH(2), n=2-7, in aqueous solvent at 10(+/-1) degrees C. In contrast to other techniques typically used to study alpha-helices in isolation (such as nuclear magnetic resonance and circular dichroism), small-angle X-ray scattering reports on the global structure of a molecule and, as such, provides complementary information to these other, more sequence-local measuring techniques. The radii of gyration that we measure are, except for the 12-mer, lower than the radii of gyration of ideal alpha-helices or helices with frayed ends of the equivalent sequence-length. For example, the measured radius of gyration of the 37-mer is 14.2(+/-0.6)A, which is to be compared with the radius of gyration of an ideal 37-mer alpha-helix of 17.6A. Attempts are made to analyze the origin of this discrepancy in terms of the analytical Zimm-Bragg-Nagai (ZBN) theory, as well as distributed computing explicit solvent molecular dynamics simulations using two variants of the AMBER force-field. The ZBN theory, which treats helices as cylinders connected by random walk segments, predicts markedly larger radii of gyration than those measured. This is true even when the persistence length of the random walk parts is taken to be extremely short (about one residue). Similarly, the molecular dynamics simulations, at the level of sampling available to us, give inaccurate values of the radii of gyration of the molecules (by overestimating them by around 25% for longer peptides) and/or their helical content. We conclude that even at the short sequences examined here (< or =37 amino acid residues), these alpha-helical peptides behave as fluctuating semi-broken rods rather than straight cylinders with frayed ends.

Circular Dichroism↗

PubMed1998

Structural characterization of the pressure-denatured state and unfolding/refolding kinetics of staphylococcal nuclease by synchrotron small-angle X-ray scattering and Fourier-transform infrared spectroscopy.

The pressure-induced unfolding of wild-type staphylococcal nuclease (Snase WT) was studied using synchrotron X-ray small-angle scattering (SAXS) and Fourier-transform infrared (FT-IR) spectroscopy, which monitor changes in the tertiary and secondary structural properties of the protein upon pressurization. The experimental results reveal that application of high-pressure up to 3 kbar leads to an approximate twofold increase of the radius of gyration Rg of the native protein (Rg approximately 17 A) and a large broadening of the pair-distance-distribution function, indicating a transition from a globular to an ellipsoidal or extended chain structure. Analysis of the FT-IR amide I' spectral components reveals that the pressure-induced denaturation process sets in at 1.5 kbar at 25 degrees C and is accompanied by an increase in disordered and turn structures while the content of beta-sheets and alpha-helices drastically decreases. The pressure-induced denatured state above 3 kbar retains nonetheless some degree of beta-like secondary structure and the molecule cannot be described as a fully extended random coil. Temperature-induced denaturation involves a further unfolding of the protein molecule which is indicated by a larger Rg value and significantly lower fractional intensities of IR-bands associated with secondary-structure elements. In addition, we have carried out pressure-jump kinetics studies of the secondary-structural evolution and the degree of compactness in the folding/unfolding reactions of Snase. The effect of pressure on the kinetics arises from a larger positive activation volume for folding than for unfolding, and leads to a significant slowing down of the folding rate with increasing pressure. Moreover, the system becomes two-state under pressure. These properties make it ideal for probing multiple order parameters in order to compare the kinetics of changes in secondary structure by pressure-jump FT-IR and chain collapse by pressure-jump SAXS. After a pressure jump from 1 bar to 2.4 kbar at 20 degrees C, the radius of gyration increases in a first-order manner from 17 A to 22.4 A over a timescale of approximately 30 minutes. The increase in Rg value is caused by the formation of an extended (ellipsoidal) structure as indicated by the corresponding pair-distance-distribution function. Pressure-jump FT-IR studies reveal that the reversible first order changes in beta-sheet, alpha-helical and random structure occur on the same slow timescale as that observed for the scattering curves and for fluorescence. These studies indicate that the changes in secondary structure and chain compactness in the folding/unfolding reactions of Snase are probably dependent upon the same rate-limiting step as changes in tertiary structure.

Kinetics↗

PubMed1990

Dynamic mechanism of the self-assembly process of tobacco mosaic virus protein studied by rapid temperature-jump small-angle X-ray scattering using synchrotron radiation.

The self-assembly process of tobacco mosaic virus protein (TMVP) was observed by rapid temperature-jump time-resolved solution X-ray small-angle scattering using synchrotron radiation. The temperature-jump device used for the X-ray measurements is rapid enough to cope with even the fastest-assembling process of TMVP, and accumulates data of reasonable signal-to-noise ratios with a minimum total counting time of 7.5 seconds. The measurements suggested that the 20 S disk of TMVP polymerized to stacked disks (short rods). The time to complete stacking varied from approximately 25 seconds to approximately 1200 seconds, depending on the solution condition and magnitude of the temperature gap. Higher protein concentration, ionic strength and temperature favoured faster association. The results were analysed in terms of a set of kinetic equations that describe the two-stage aggregation of TMVP with an equilibrium constant K1, and two rate constants k+2 and k-2 for association and dissociation of disks, respectively. The consistency of the analysis suggests that the TMVP assembly proceeds in two steps of: (1) the aggregation of A-proteins into double-layered disks; and (2) the stacking of double-layered disks. The kinetic analysis indicated that the stacking belongs to the lowest range of protein-protein interaction system.

Capsid Proteins↗

PubMed1992

4Ca2+.troponin C forms dimers in solution at neutral pH that dissociate upon binding various peptides: small-angle X-ray scattering studies of peptide-induced structural changes.

Small-angle X-ray scattering data have been measured for rabbit skeletal muscle troponin C and its complexes with the venom peptides melittin and mastoparan as well as synthetic peptides based on regions of the troponin I sequence implicated in troponin C binding. At the neutral pH used in this study (pH 6.8), troponin C shows a tendency to form dimers in the presence of 4 mol equiv of Ca2+, but is monomeric in solution when 2 or less mol equiv of Ca2+ is present. The 4Ca2+.troponin C dimers dissociate upon binding melittin, mastoparan, and peptides based on residues 96-115, 1-30, and 1-40 in the troponin I sequence. This result suggests that the peptide-binding sites overlap with the regions of contact between troponin C molecules forming a dimer. Like the structurally homologous calcium-binding protein calmodulin, troponin C shows conformational flexibility upon binding different peptides. Upon binding melittin, troponin C contracts in a similar manner to calmodulin when it binds peptides known to form amphiphilic helices (e.g., melittin, mastoparan, or MLCK-I). In contrast, mastoparan binding to troponin C does not result in a contracted structure. The scattering data indicate troponin C also remains in an extended structure upon binding the inhibitory peptides having the same sequence as residues 96-115 in troponin I.

Amino Acid Sequence↗

PubMed1979

Spermine-DNA complexes build up metastable structures. Small-angle X-ray scattering and circular dichroism studies.

Spermine-DNA complexes have been examined by small-angle and wide-angle X-ray scattering as well as by circular dichroism studies. Condensed complexes are building up below a critical ionic strength. We have found that at one and the same ionic strength condensed complexes having two different supramolecular structures (Type I and Type II) can coexist. The structure of the condensates depends on the method of condensate formation. Phase transitions between these structures can be induced by thermal treatment. We conclude from these facts that with polyamine-DNA condensates metastable structures are of importance.

Animals↗

PubMed2001

Unraveling double stranded alpha-helical coiled coils: an x-ray diffraction study on hard alpha-keratin fibers.

Transformations of proteins secondary and tertiary structures are generally studied in globular proteins in solution. In fibrous proteins, such as hard alpha-keratin, that contain long and well-defined double stranded alpha-helical coiled coil domains, such study can be directly done on the native fibrous tissue. In order to assess the structural behavior of the coiled coil domains under an axial mechanical stress, wide angle x-ray scattering and small angle x-ray scattering experiments have been carried out on stretched horse hair fibers at relative humidity around 30%. Our observations of the three major axial spacings as a function of the applied macroscopic strain have shown two rates. Up to 4% macroscopic strain the coiled coils were slightly distorted but retained their overall conformation. Above 4% the proportion of coiled coil domains progressively decreased. The main and new result of our study is the observation of the transition from alpha-helical coiled coils to disordered chains instead of the alpha-helical coiled coil to beta-sheet transition that occurs in wet fibers.

Animals↗

PubMed1983

Time-resolved small-angle X-ray scattering experiment on association of isolated alpha- and beta-chains of human hemoglobin.

The time course of the recombination of hemoglobin from isolated alpha- and beta-chains (human) was studied by following the change in small-angle scattering from a reaction mixture using synchrotron radiation. The scattering patterns were recorded successively within 51 s at intervals of 200 ms. The results suggest that when 2 mM solutions of CO-liganded alpha- and beta-chains are mixed in stoichiometric amounts at pH 7.4, the tetramerization process is a pseudo-first-order reaction with a rate constant of 0.059 s-1, i.e., a half-time of approx. 12 s.

Hemoglobins↗

PubMed2003

A systematic study of bovine serum albumin (BSA) and sodium dodecyl sulfate (SDS) interactions by surface tension and small angle X-ray scattering.

Classical parameters obtained from surface tension technique coupled to small angle X-ray scattering (SAXS) measurements gave support to investigate conformational changes in the bovine serum albumin (BSA)-sodium dodecyl sulfate (SDS) complexes, as well as the size of the micelle-like clusters distributed along the polypeptide chain. The studied systems were composed of 1 wt% of BSA in the absence and presence of increasing SDS molar concentration up to 80 mM, under experimental conditions of low ionic strength and pH 5.40. At SDS concentrations below the critical aggregation concentration (cac) of 2.2 mM, SAXS results indicate that the detergent does not modify the native protein conformation. However, the beginning of protein unfolding, evidenced by SAXS through an increase in the values of radius of gyration Rg and protein maximum dimension Dmax, is coincident with the onset of SDS cooperative binding to BSA identified by the first breakpoint in the surface tension-SDS profile. Further SDS addition leads to the formation of micelle-like aggregates randomly distributed along the unfolded polypeptide chain, consistent to a necklace and bead model. The SAXS data also demonstrate that the SDS micelles grow in size up to 50 mM detergent. At 50 mM surfactant, the micelles stop growing. This concentration is near the BSA saturation binding by SDS measured by dialyzes and indicated by the second breakpoint in surface tension-SDS profile. The SAXS and surface tension data are also consistent with the formation of free micelles in equilibrium with BSA-SDS complexes for surfactant amount above the saturation.

Animals↗

PubMed1992

Small-angle X-ray-scattering studies of the C hordeins of barley (Hordeum vulgare).

Small angle X-ray scattering was used to study the solution conformation of the C hordeins of barley (Hordeum vulgare), a group of proteins whose primary structure consists predominantly of an octapeptide repeat motif. Measurements on the protein in 0.1 M-acetic acid at 25 degrees C are consistent with a model for the protein conformation of a stiff coil, the so-called 'worm-like' chain. The characteristic parameters (the Kuhn statistical segment length and the contour length) of the protein were calculated as 5.11 and 71.5 nm respectively.

Glutens↗

PubMed1980

Small-angle x-ray scattering studies of thermally-induced globular protein gels.

Small-angle X-ray scattering has been applied to gels formed by heating globular proteins, in aqueous solution, above their unfolding temperatures. A number of BSA gels, previously characterized by electron microscopy, have been studied, and, by setting up theoretical models for the scattering process, the X-ray data have been shown to be consistent with the microscope conclusions regarding network structure. It is concluded that the networks form by a linearly-directed aggregation of unfolded, disc-like, protein molecules, three-dimensional geometry being achieved by occasional branching, and/or cross-linking. Long-range inhomogeneities in network structure, easily observed by electron microscopy, and correlated with variations in pH or ionic strength, have an effect on X-ray scattering, and hence the x-ray method is sensitive not only to different network strand thicknesses, but to different degrees of uniformity as well.

Animals↗

PubMed1996

Dynamic Small-Angle X-ray Scattering System using an Imaging Plate.

A synchrotron-radiation dynamic small-angle X-ray scattering (Synchrotron Radiation-DSAXS) system using an imaging plate has been developed at the Photon Factory, National Laboratory for High Energy Physics, Japan, in collaboration with the Department of Polymer Chemistry, Kyoto University, Japan, for studying the dynamic response of mesoscopic structures in polymers to applied mechanical stimuli. Small-angle X-ray scattering patterns of 100 x 100 mm(2) have been successively recorded on a 400 x 200 mm(2) stage-mounted imaging plate with a minimum time interval of 0.5 s. X-ray data are simultaneously obtained with stress and strain measurements on specimens subjected to a mechanical deformation. The performance of the DSAXS system is demonstrated along with some experimental results concerning the dynamic deformation of a b.c.c. lattice with paracrystalline distortion in a co-polymer having spherical microdomains under a large oscillatory shear deformation.

Journal Article↗

PubMed1991

Ultra-small-angle x-ray-scattering study: preliminary experiments in colloidal suspensions.

We report here a multiple-reflection type ultra-small-angle x-ray-scattering apparatus constructed according to the principle proposed by Bonse and Hart. The ultra-small-angle x-ray scattering technique enables us to investigate the distribution of solutes or particles in turbid systems, which could not be studied by the conventional light-scattering and microscopic methods. By this method, the density fluctuation from an order of several thousand angstroms to several micrometers is now detectable. In this paper, the ultra-small-angle x-ray scattering apparatus was calibrated by using well-defined latex particles.

Journal Article↗

PubMed2004

Synchrotron radiation small- and wide- angle scattering study of dispergation of Equoral, a novel drug delivery system with cyclosporine A.

Equoral oral solution is a novel drug delivery system for cyclosporine consisting mainly of non-ionic surfactants, polyglycerol esters and polyoxyethylated fatty acids aggregates, and gives microdispersions in the aqueous enviroment. To simulate dispergation, Equoral was mixed with varying amounts of water. Changes in the structure of the prepared aggregates were studied using synchrotron x-ray small- and wide-angle scattering. A lamellar phase is the most probable structure, arising spontaneously after dispergation of Equoral in the region of 30-70 wt% H2O.

Cyclosporine↗

PubMed1999

Conformation of poly(methacrylic acid) in acidic aqueous solution studied by small angle X-ray scattering.

The nature of the contracted form of poly(methacrylic acid) PMA chain in salt-free acidic aqueous solution was studied by analyzing scattering curves registered by small-angle X-ray scattering, comparing it with those of PMA in methanol at 26 degrees C and of partially neutralized PMA in aqueous solution containing added salt (the concentration of added salt, Cs=0.1 M NaF). It is shown that the distribution of segments in the contracted form as well as that of PMA in methanol is that of a random-coil in a theta medium and that this distribution of segments is stable over a fair range of degrees of ionization alpha for Cs below 0.1 M. Moreover, the persistence length of PMA at Cs=0.1 M (4+/-0.5 A) is substantially constant throughout the entire range of alpha, indicating that the contracted form of PMA changes to an expanded random-coil in a higher pH region without a significant change in the chain flexibility.

Journal Article↗