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Results for “Scattering, Small Angle”

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PubMed2000

Small angle X-ray scattering studies on local structure of tobacco mosaic virus RNA in solution.

Effects of temperature and ionic strength (S) on the local structure of tobacco mosaic virus RNA in phosphate buffer solution are studied by analyzing the small-angle X-ray scattering (SAXS) curves. The root-mean-square radius of a cross-section of RNA chain was kept at 0.845+/-0.005 nm over a wide range of S from 0.2 to 0.003 at 20 degrees C, whereas it gradually diminished from 0.85 to 0.61 nm when the temperature is raised from 20 to 50 degrees C at S = 0.2. Nevertheless, all of SAXS curves reflecting the backbone structures were equally mimicked by theoretical ones of freely hinged rod (FHR) models, i.e. several straight rods joined with freely hinged joints in the form of a combination of the letter Y, if the constituent rod lengths in the models are adjusted. From these facts, it is suggested that the local structure of the RNA chain in aqueous solution is characterized by an essential feature that unpaired bases in the partially double-stranded helix are constantly far isolated from each other along the helix and the rod-like structure of the helix is preserved over a range of helical contents. Such a characteristic local structure of the chain is entirely collapsed in the formamide solution at 50 degrees C.

Buffers↗

PubMed2002

Solution structure of human and bovine beta(2)-glycoprotein I revealed by small-angle X-ray scattering.

beta(2)-Glycoprotein I (beta(2)GPI) is a highly glycosylated phospholipid-binding plasma protein comprised of four complement control protein (CCP) domains and a distinct fifth domain. The structural organisation of human and bovine beta(2)GPI in aqueous solution was studied by small-angle X-ray scattering (SAXS). Low-resolution models that match the SAXS experimental data best were independently constructed by three different ab initio 3D-reconstruction algorithms. Similar elongated S-shaped models with distinct side-arms, which were correlated to the position of the carbohydrate chains, were restored from all three algorithms. Due to an additional glycosylation site located on the CCP2 domain of bovine beta(2)GPI a small change in the characteristic SAXS parameters was observed, which coincided with results obtained from SDS-PAGE. In comparison to the human analogue the corresponding restored low-resolution models displayed a similar S-shape with less bending in the middle part. As the experimental SAXS curves fit poorly to the simulated scattering curves calculated from the crystallographic coordinates of human beta(2)GPI, the crystal structure was modified. First, additional carbohydrate residues missing from the crystal structure were modelled. Second, on the basis of the low-resolution models, the J-shaped crystal structure was rotated between CCP3 and CCP2 assuming the greatest interdomain flexibility between these domains. An S-shaped model with a tilt angle of approximately 60 degrees between CCP3 and CCP2 yielded the best fit to the experimental SAXS data. Since there is evidence that beta(2)GPI can adopt different conformations, which reveal distinct differences in autoantibody recognition, our data clearly point to a reorientation of the flexible domains, which may be an essential feature for binding of autoantibodies.

Algorithms↗

PubMed1996

Small-angle X-ray scattering of kappa- and iota-carrageenan in aqueous and in salt solutions.

Aqueous and saline (0.03-0.08 M NaCl) solutions of the Na(+)-salt of kappa- and iota-carrageenan (3-17 mg/ml) have been investigated using small-angle X-ray scattering (SAXS). Investigation of the SAXS curves normalized for concentration allows to detect the transition from the dilute to the semidilute regime. Some of the experimental curves exhibit a clear maximum. In the case of kappa-carrageenan, the position of this maximum is proportional to the cube root of polysaccharide concentration. The fluctuation theory of Borue and Erukhimovich (BE theory), which predicts a maximum in the scattering curves for low ionic strength, gives a good fit for all our experiments. An increase of the polymer concentration or the ionic strength causes the appearance of two subsystems in solution exhibiting a different characteristic screening scale of Coulombic interaction for ideal Gaussian chains (and two different segment lengths). The condition for an increase of the relative contribution of the subsystem with the larger segment length correlates with the one for the disorder-order transition of carrageenan. In the most concentrated (17.1 mg/ml) solution of Na(+)-iota-carrageenan, the increase of NaCl molarity above 0.06 M gives rise to additional scattered intensity at the smallest angles, indicating molecular association.

Carrageenan↗

PubMed2004

Conformation of poly(sodium ethacrylate) in solution studied by small-angle X-ray scattering.

The pH-induced conformational transition of poly(sodium ethacrylate) PNaEA in aqueous solution, which occurs between a compact form at low charge-density and an extended coil at high charge-density, was studied by small-angle X-ray scattering and the structure at an each conformational state was analyzed and compared with the corresponding one of poly(sodium methacrylate) PNaMA. The conformational transition for PNaEA induced a remarkable change in the scattering data plotted in the form of the Kratky plot. By comparing the scattering data with theoretical scattering functions, it was clarified that the structures of the compact form and the extended coil are well mimicked by a swollen gel having a network structure and by a wormlike chain, respectively. Although such a structure of the extended coil of PNaEA is similar to the corresponding one of PNaMA, the structure of the compact form of PNaEA is different from the corresponding one of PNaMA, which is still represented by a wormlike chain in a Theta medium.

Ethacrynic Acid↗

PubMed1999

Reversibility and hierarchy of thermal transition of hen egg-white lysozyme studied by small-angle x-ray scattering.

To clarify mechanisms of folding and unfolding of proteins, many studies of thermal denaturation of proteins have been carried out at low protein concentrations because in many cases thermal denaturation accompanies a great tendency of aggregation. As small-angle x-ray scattering (SAXS) measurements are liable to use low-concentration solutions of proteins to avoid aggregation, SAXS has been regarded as very difficult to observe detailed features of thermal structural transitions such as intramolecular structural changes. By using synchrotron radiation SAXS, we have found that the presence of repulsive interparticle interaction between proteins can maintain solute particles separately to prevent further aggregation in thermal denaturation processes and that under such conditions the thermal structural transition of hen egg-white lysozyme (HEWL) holds high reversibility even at 5% w/v HEWL below pH approximately 5. Because of the use of the high concentration of the solutions, the scattering data has enough high-statistical accuracy to discuss the thermal structural transition depending on the structural hierarchy. Thus, the tertiary structural change of HEWL starts from mostly the onset temperature determined by the differential scanning calorimetry measurement, which accompanies a large heat absorption, whereas the intramolecular structural change, corresponding to the interdomain correlation and polypeptide chain arrangement, starts much prior to the above main transition. The present finding of the reversible thermal structural transitions at the high protein concentration is expected to enable us to analyze multiplicity of folding and unfolding processes of proteins in thermal structural transitions.

Animals↗

PubMed1976

Molecular model for 5-S RNA. A small-angle x-ray scattering study of native, denatured and aggregated 5-S RNA from Escherichia coli ribosomes.

A tertiary structural model is suggested for Escherichia coli 5-S RNA that consists of one large and two small double helices arranged in the form of the letter Y. This model is consistent with the small-angle X-ray scattering data of native 5-S RNA, measured in the angular range 20 less than or equal to 140 mrad. The radium of gyration is 3.61 +- 0.1 Nm. Denatured 5-S RNA yields a much lower radius of gyration, 2.7 nm, which might indicate that during denaturation one minor double-helical arm of the Y-shaped structure partially collapses into single-stranded areas. At high concentrations (60 mg/ml) of 5-S RNA, the X-ray scattering data indicate that 5-S RNA is aggregated.

Base Sequence↗

PubMed2025

Biochemical and Structural Analyses of the Tardigrade DNA-Damage Suppressor Protein, Dsup.

Tardigrades are extremophiles that withstand harsh environments through unique molecular strategies. One such strategy involves Damage Suppressor (Dsup), a protein shown to protect cells from radiation-induced DNA damage. Little is known about the biochemical and structural characteristics of Dsup that lead to DNA protection. To gain insight into the mechanism of DNA protection by Dsup, we examined its fundamental biochemical and structural properties using mass photometry, biolayer interferometry, small-angle X-ray scattering, and microfluidic modulation spectroscopy. We found that Dsup is largely intrinsically disordered and binds DNA with high affinity via a multi-valent interface. This interaction induced conformational changes in both Dsup and the DNA, suggesting a potential structural mechanism of its DNA protection ability. We propose that Dsup alters DNA structure, possibly by partially unwinding it, to reduce its susceptibility to damage. These findings offer new insights into how a disordered protein such as Dsup functions as radioprotectants in extreme environments.

Tardigrada↗

PubMed2006

X-ray intensity fluctuation spectroscopy by heterodyne detection.

A straightforward way of measuring X-ray intensity fluctuation spectroscopy in a small-angle X-ray scattering configuration is demonstrated using heterodyne techniques. Two examples are presented: the Brownian motion of latex spheres in glycerol, and a Doppler velocity experiment demonstrating the motion and the relaxation of carbon-black-filled elastomers after uniaxial stretching. In the latter case the effects of mechanical relaxation can be separated from those of aggregate diffusion. The results suggest that the dynamics of these filled elastomers are similar to the universal features observed in disordered jammed systems.

Algorithms↗

PubMed2005

Evidence of the hexagonal columnar liquid-crystal phase of hard colloidal platelets by high-resolution SAXS.

We report Small-Angle X-ray Scattering (SAXS) measurements of the columnar phase of hard colloidal gibbsite platelets. We have been able to create large oriented domains of the columnar phase both perpendicular and parallel to the sample wall, varying the volume fraction of platelets and adding non-adsorbing polymer to the dispersion. In conjunction with the increased resolution of the SAXS setup, this allowed a detailed analysis of the columnar phase, providing unambiguous evidence for the hexagonal nature of the phase.

Colloids↗

PubMed2003

Small angle x-ray scattering of the hemoglobin from Biomphalaria glabrata.

The hemoglobin from Biomphalaria glabrata is an extracellular respiratory protein of high molecular mass composed by subunits of 360 kDa, each one containing two 180 kDa chains linked by disulfide bridges. In this work, small angle x-ray scattering (SAXS) measurements were performed with the hemoglobin at pH 5.0 and 7.5. Radii of gyration of 98.6 +/- 0.5 and 101.8 +/- 0.2 A and maximum diameters of 300 +/- 10 and 305 +/- 10 A, respectively, were obtained from Guinier plot extrapolation and analytical curve fitting. The pair distance distribution functions p(r) corresponded to globular particles with a somewhat anisotropic shape for both preparations. Computer analysis of the low angle part of the scattering curve led to the determination of the low resolution envelope of the protein, revealing a P(222) symmetry. Shape reconstruction from ab initio calculations using the complete scattering curve furnished a compact prolate three-dimensional (3D) bead model for the protein. Hydrodynamic parameters were obtained from experiments and theoretical calculations using the 3D model. The results of the structural and biochemical studies reported herein indicate that the multisubunit structure of this hemoglobin is compatible with a tetrameric arrangement.

Animals↗

PubMed2006

Interfacial surface charge and free accessibility to the PLA2-active site-like region are essential requirements for the activity of Lys49 PLA2 homologues.

Lys49 phospholipase A2 homologues are highly myotoxic and cause extensive tissue damage but do not display hydrolytic activity towards natural phospholipids. The binding of heparin, heparin derivatives and polyanionic compounds such as suramin result in partial inhibition (up to 60%) of the myotoxic effects due to a change in the overall charge of the interfacial surface. In vivo experiments demonstrate that polyethylene glycol inhibits more than 90% of the myotoxic effects without exhibiting secondary toxic effects. The crystal structure of bothropstoxin-I complexed with polyethylene glycol reveals that this inhibition is due to steric hindrance of the access to the PLA2-active site-like region. These two inhibitory pathways indicate the roles of the overall surface charge and free accessibility to the PLA2-active site-like region in the functioning of Lys49 phospholipases A2 homologues. Molecular dynamics simulations, small angle X-ray scattering and structural analysis indicate that the oligomeric states both in solution and in the crystalline states of Lys49 phospholipases A2 are principally mediated by hydrophobic contacts formed between the interfacial surfaces. These results provide the framework for the potential application of both clinically approved drugs for the treatment of Viperidae snakebites.

Animals↗

PubMed2007

Ca2+- and ba2+-ligand coordinated unilamellar, multilamellar, and oligovesicular vesicles.

Ca(2+)- and Ba(2+)-coordinated vesicle phases were prepared in mixed aqueous solutions of tetradecyldimethylamine oxide (C(14)DMAO) and calcium oleate (Ca(OA)(2)) or barium oleate (Ba(OA)(2)). At the right mixing ratios, metal-ligand coordination between Ca(OA)(2) or Ba(OA)(2) and C(14)DMAO results in the formation of molecular bilayers due to the reduction in area per head group. Ca(2+) and Ba(2+) tightly associate to the head groups of surfactants and in this system the bilayer membranes are not shielded by excess salts. The structures of the birefringent samples of the Ca(OA)(2)/C(14)DMAO/H(2)O and Ba(OA)(2)/C(14)DMAO/H(2)O systems were determined by freeze-fracture transmission electron microscopy (FF-TEM), small-angle X-ray scattering (SAXS), and rheological measurements to consist of unilamellar, multilamellar, and oligovesicular vesicles. The coordination between C(14)DMAO and Ba(OA)(2) or Ca(OA)(2) plays an important role in the formation of the vesicles, which was easily confirmed by studying the phase behavior of the KOA/C(14)DMAO/H(2)O system in which only the L(1) phase forms, due to the absence of coordination between KOA and C(14)DMAO. A mechanism is proposed that accounts for the formation of these new metal-ligand coordinated vesicles.

Barium↗

PubMed2006

Autoreduction and aggregation of fungal laccase in solution phase: possible correlation with a resting form of laccase.

This paper reports results of a reexamination of some poorly understood peculiarities of laccases, an enzyme family which has been extensively studied in our laboratories as well as by others for some years. The issue that is reconsidered here is the previously proposed existence of "active" and "resting" forms of laccases. The presence of fungal laccases with partly reduced active sites is demonstrated. Of further interest is that an aggregated state in solution, not to our knowledge previously noted for laccase, has been found by using small-angle X-ray scattering as well as thorough analysis of the results of several biochemical experiments. Under some conditions, this aggregated state may correlate with the resting form of the laccases, although this resting form could have a broader significance. It was shown that Trametes ochracea laccase had some anomalous characteristics, which could be correlated with the high concentration of the "resting" enzyme. The mechanism of formation of resting laccase is suggested. Knowledge of the resting state is of importance for in vitro studies. Additionally, a suggestion about the possible regulatory role of this form in vivo is mentioned.

Basidiomycota↗

PubMed2006

Microstructure and rheological properties of liquid crystallines formed in Brij 97/water/IPM system.

The phase diagram of Brij 97/water/IPM systems was determined at 25 degrees C. Rich liquid crystalline phases including Lalpha, H1, and cubic Fd3m phases were identified by means of small angle X-ray scattering (SAXS). Microstructure transitions of liquid crystals with changes in surfactant concentration and oil content are explained qualitatively by the surfactant packing parameter (vL/aSlc). Dynamic rheological results indicate that all three kinds of liquid crystals investigated show high elasticity. The lamellar, Lalpha, phases formed in Brij 97/water with two different oils, oleic acid and geraniol, were also studied in comparison with those of Brij 97/water/IPM systems. The strength of the network of lamellar phases formed in Brij 97/water/oleic acid and Brij 97/water/geraniol systems are appreciably stronger than for Brij 97/water/IPM systems, indicated by the smaller area of surfactant molecules at the interface and the higher moduli (G' and G'').

Liquid Crystals↗

PubMed2026

A protein-dependent riboswitch activates ribosomal frameshifting in cardioviruses.

Programmed -1 ribosomal frameshifting (PRF) is a translational control mechanism used by RNA viruses to regulate the relative abundance of proteins encoded in different reading frames. Cardioviruses exhibit the highest known PRF efficiency, with ∼85% of ribosomes shifting into the -1 frame. This unusual event requires an interaction between the viral 2A protein and a stimulatory element in the RNA genome, but the basis for protein dependence is unclear. To address this, here we investigate the structure and dynamics of the PRF signal in Theiler's murine encephalitis virus (TMEV). By combining X-ray crystallography, small-angle X-ray scattering (SAXS), and single-molecule fluorescence resonance energy transfer (smFRET), we show that 2A binding switches the RNA from a stem-loop conformation into a pseudoknot, and we demonstrate that pseudoknot formation is essential for efficient PRF in vitro and in cells. Together, these findings illustrate how the cardiovirus PRF element behaves as a protein-dependent riboswitch, defining the molecular mechanism by which frameshifting is conditionally activated.

Frameshifting, Ribosomal↗

PubMed2006

Association of vasoactive intestinal peptide with polymer-grafted liposomes: structural aspects for pulmonary delivery.

A polymer-grafted liposomal formulation that has the potential to be developed for aerosolic pulmonary delivery of vasoactive intestinal peptide (VIP), a potent vasodilatory neuropeptide, is described. As VIP is prone to rapid proteolytic degradation in the microenvironment of the lung a proper delivery system is required to increase the half-life and bioavailability of the peptide. Here we investigate structural parameters of unilamellar liposomes composed of palmitoyl-oleoyl-phosphatidylcholine, lyso-stearyl-phosphatidylglycerol and distearyl-phosphatidyl-ethanolamine covalently linked to polyethylene glycol 2000, and report on VIP-lipid interaction mechanisms. We found that the cationic VIP is efficiently entrapped by the negatively charged spherical liposomes and becomes converted to an amphipathic alpha-helix. By fluorescence spectroscopy using single Trp-modified VIP we could show that VIP is closely associated to the membrane. Our data suggest that the N-terminal random-coiled domain is embedded in the interfacial headgroup region of the phospholipid bilayer. By doing so, neither the bilayer thickness of the lipid membrane nor the mobility of the phospholipid acyl chains are affected as shown by small angle X-ray scattering and electron spin resonance spectroscopy. Finally, in an ex vivo lung arterial model system we found that liposomal-associated VIP is recognized by its receptors to induce vasodilatory effects with comparable high relaxation efficiency as free VIP but with a significantly retarded dilatation kinetics. In conclusion, we have designed and characterized a liposomal formulation that is qualified to entrap biologically active VIP and displays structural features to be considered for delivery of VIP to the lung.

Administration, Inhalation↗

PubMed2004

Structural evolution of regenerated silk fibroin under shear: combined wide- and small-angle x-ray scattering experiments using synchrotron radiation.

The structural evolution of regenerated Bombyx mori silk fibroin during shearing with a Couette cell has been studied in situ by synchrotron radiation small- and wide-angle x-ray scattering techniques. An elongation of fibroin molecules was observed with increasing shear rate, followed by an aggregation phase. The aggregates were found to be amorphous with beta-conformation according to infrared spectroscopy. Scanning x-ray microdiffraction with a 5 microm beam on aggregated material, which had solidified in air, showed silk II reflections and a material with equatorial reflections close to the silk I structure reflections, but with strong differences in reflection intensities. This silk I type material shows up to two low-angle peaks suggesting the presence of water molecules that might be intercalated between hydrogen-bonded sheets.

Fibroins↗

PubMed2005

Influence of initial order on the microscopic mechanism of electric field induced alignment of block copolymer microdomains.

We investigate the mechanism of microdomain orientation in concentrated block copolymer solutions exposed to a dc electric field by in situ synchrotron small-angle X-ray scattering (SAXS). As a model system, we use concentrated solutions of a lamellar polystyrene-b-polyisoprene block copolymer in toluene. We find that both the microscopic mechanism of reorientation and the kinetics of the process strongly depend on the initial degree of order in the system. In a highly ordered lamellar system with the lamellae being aligned perpendicular to the electric field vector, only nucleation and growth of domains is possible as a pathway to reorientation and the process proceeds rather slowly. In less ordered samples, grain rotation becomes possible as an alternative pathway, and the process proceeds considerably faster. The interpretation of our finding is strongly corroborated by dynamic self-consistent field simulations.

Electricity↗