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PubMed1990

Structure of human low-density lipoprotein subfractions, determined by X-ray small-angle scattering.

The structure of low-density lipoprotein (LDL) particles from three different density ranges (LDL-1: d = 1.006-1.031 g/ml; LDL-3: d = 1.034-1.037 g/ml; LDL-6: d = 1.044-1.063 g/ml) was determined by X-ray small-angle scattering. By using a theoretical particle model, which accounted for the polydispersity of the samples, we were able to obtain fits of the scattering intensity that were inside the noise interval of the measured intensity. The assumption of deviations from radial symmetry is not supported by our data. This implies a spread-out conformation of the apolipoprotein B (apoB) molecule, which appears to be localized in the outer surface shell. A globular structure is not consistent with our data. Furthermore, different models exist concerning the structure of the cholesterol ester core below the phase transition temperature. The electron density data suggest an arrangement in which the steroid moieties are localized at average radii of 3.2 and 6.4 nm. Model calculations show that packing problems can only be avoided if approximately half of the acyl chains of each shell are pointing towards the center of the particle, the other half towards the surface. This arrangement of the acyl chains has never been proposed before. The LDL particles of different density classes differ mainly with respect to the size of the core but also with respect to the width of the surface shells. Model calculations show that the size of different LDL particles can be accurately predicted from the compositional data.

Apolipoproteins B↗
PubMed2006

A target function for quaternary structural refinement from small angle scattering and NMR orientational restraints.

We present a novel target function based on atomic coordinates that permits quaternary structural refinement of multi-domain protein-protein or protein-RNA complexes. It requires that the high-resolution structures of the individual domains are known and that small angle scattering (SAS) data as well as NMR orientational restraints from residual dipolar couplings (RDCs) of the complex are available. We show that, when used in combination, the translational and rotational restraints contained in SAS intensities and RDCs, respectively, define a target potential function that permits to determine the overall topology of complexes made up of domains with low internal symmetry. We apply the target function on a modestly anisotropic model system, the Barnase/Barstar complex, and discuss factors that influence the structural refinement such as data errors and the geometrical properties of the individual domains.

Algorithms↗
PubMed1979

Structure of the dimyristoylphosphatidylcholine vesicle and the complex formed by its interaction with apolipoprotein C-III: X-ray small-angle scattering studies.

Single bilayer vesicles of dimyristoylphosphatidylcholine have been investigated by small-angle X-ray scattering at 28 degrees C. The results indicate that these vesicles are hollow spherical shell structures with an outer radius of approximately 12 nm and a molecular weight of (3.2 +/- 0.5) X 10(6). The shell was found to be 4.4 +/- 0.2 nm thick with a cross-sectional electron-density profile characteristic for a single phospholipid bilayer. Upon interaction of these vesicles with apolipoprotein C-III from human very low density lipoproteins at a protein/lipid ratio greater than 0.08 (g/g), a complex containing 0.25 g of protein/g of lipid, with molecular weight of (3.9 +/- 0.4) X 10(5), is formed. The shape analysis indicates a highly asymmetric particle with an internal partition of low and high electron density resembling that produced by a bilayer structure. Model calculations and curve-fitting procedures show good agreement between the experimental scattering curve and that computed for an oblate ellipsoidal structure with dimensions of 17 X 17 X 5 nm and a 1 nm thick shell of high electron density surrounding the core of low electron density.

Apolipoproteins↗
PubMed1999

Small-Angle Scattering and Electron Microscopy Investigation of Nanotubules Made from a Perfluoroalkylated Glucophospholipid.

Anionic glucophospholipids were recently reported as a new family of tubule-forming lipids. We report here investigations on the structure of nanotubules made from a glucophospholipid with a mixed fluorocarbon-hydrocarbon hydrophobe, using freeze fracture and cryo-transmission electron microscopy (TEM) and X-ray and neutron small angle scattering (SAXS, SANS). The hollow and regularly shaped tubules are very thin: they have an external radius of 140 Å and an internal radius of 35 Å on the average. Their 105 Å-thick wall appears to consist in three bilayers in which the glucophospholipid molecules are probably in a tilted and/or interdigitated configuration. Upon heating these nanotubes convert reversibly into vesicles; transformation is complete at 60 degrees C. Copyright 1999 Academic Press.

Journal Article↗
PubMed1981

Structure of two subfractions of normal porcine (Sus domesticus) serum low-density lipoproteins. X-ray small-angle scattering studies.

Two subfractions of low-density lipoproteins (LDL) were isolated from normal pig (Sus domesticus) serum by a combined method including precipitation, ultracentrifugation, and gel chromatography. The fractions recovered from the buoyant density ranges 1.020-1.050 and 1.050-1.090 g/mL, denoted as LDL1 and LDL2, respectively, were studied with regard to structure and thermotropic behavior by X-ray small-angle scattering and were compared to human serum low-density lipoprotein of density 1.020-1.063 g/mL. The average molecular weights determined from the scattering intensities on absolute scale were 2.6 X 10(6) and 2.0 X 10(6) for LDL1 and LDL2, respectively. The maximum particle diameters were found to be 24 and 21 nm, respectively. Both species were found to have quasi-spherical symmetry and to display the thermotropic transition of the apolar lipids within the particle core similar to human LDL. The width of the transition was approximately 9 degrees C in both cases, but the midpoint transition temperature was higher by 8 degrees C for LDL1 (33 degrees C) than for LDL2 (25 degrees C). Despite their different sizes and thermotropic behavior, the two porcine LDL subfractions appear to be built according to the same structural principle as human LDL in the molecular organization of the apolar lipids within the particle core.

Animals↗
PubMed2004

Pressure denaturation of staphylococcal nuclease studied by neutron small-angle scattering and molecular simulation.

We studied the pressure-induced folding/unfolding transition of staphylococcal nuclease (SN) over a pressure range of approximately 1-3 kilobars at 25 degrees C by small-angle neutron scattering and molecular dynamics simulations. We find that applying pressure leads to a twofold increase in the radius of gyration derived from the small-angle neutron scattering spectra, and P(r), the pair distance distribution function, broadens and shows a transition from a unimodal to a bimodal distribution as the protein unfolds. The results indicate that the globular structure of SN is retained across the folding/unfolding transition although this structure is less compact and elongated relative to the native structure. Pressure-induced unfolding is initiated in the molecular dynamics simulations by inserting water molecules into the protein interior and applying pressure. The P(r) calculated from these simulations likewise broadens and shows a similar unimodal-to-bimodal transition with increasing pressure. The simulations also reveal that the bimodal P(r) for the pressure-unfolded state arises as the protein expands and forms two subdomains that effectively diffuse apart during initial stages of unfolding. Hydrophobic contact maps derived from the simulations show that water insertions into the protein interior and the application of pressure together destabilize hydrophobic contacts between these two subdomains. The findings support a mechanism for the pressure-induced unfolding of SN in which water penetration into the hydrophobic core plays a central role.

Algorithms↗
PubMed2006

Small-angle scattering from hexagonal liquid crystals.

In this paper, we discuss the scattering behavior of two-dimensional hexagonal liquid crystals with micellar cylinders as a building unit. We treat the hexagonal phase as an accumulation of ordered domains of finite size that typically consists of one hundred parallel cylinders whose axes are perpendicular to the lattice plane. When we suppose that no specific orientation is preferred, the lengths of the cylinders are rather large compared to their diameter, and the polydispersity of the size of the cylinders is negligible; it is therefore possible to split the scattering intensity into a product of the so-called form factor and the structure factor. This product approximation is the basic condition for the use of the generalized indirect Fourier transformation (GIFT) method and the deconvolution (DECON) method to evaluate the small-angle scattering data of hexagonal phases. The GIFT method provides the parameters of the structure factor model and the pair distance distribution function of the cylinders. Via the DECON technique, we can calculate the radial contrast profile of the cylinders from the pair distance distribution function that is obtained by the GIFT method.

Journal Article↗
PubMed1983

Neutron small angle scattering of matched proteoliposomes with incorporated F0F1 ATPase complex from Rhodospirillum rubrum FR1. An approach to the structure of membrane proteins in their natural environment.

Purified F0F1 ATPase from Rhodospirillum rubrum FR1 has been incorporated into lipid vesicles from the partially deuterated phospholipid dimyristoylglycerophosphocholine (DMPC-D54). These proteoliposomes were able to carry out energy transducing reactions. The incorporation of the membrane protein was controlled by freeze fracture electron microscopy. A method for structural research of the membrane protein in its natural environment has been developed by means of neutron small angle scattering. Using the contrast variation technique, the lipid part of the proteoliposomes was matched by adding an appropriate amount of D2O to the solvent. Thus the neutron scattering profile of F0F1 ATPase incorporated into vesicles was separated from the neutron scattering of the liposome. F0F1 ATPase incorporated in a lipid bilayer, as well as the free enzyme, yields a radius of gyration of Rg = 6.0 +/- 0.1 nm which leads to an overall diameter of 15.5 nm. This result suggests that the monomeric form of F0F1 ATPase is incorporated in DMPC-D54 membranes at 20 degrees C.

Adenosine Triphosphatases↗
PubMed2007

Interphase effects in dental nanocomposites investigated by small-angle neutron scattering.

Small-angle and ultrasmall-angle neutron scattering (SANS and USANS) were used to characterize silica nanoparticle dispersion morphologies and the interphase in thermoset dimethacrylate polymer nanocomposites. Silica nanoparticle fillers were silanized with varying mass ratios of 3-methacryloxypropyltrimethoxysilane (MPTMS), a silane that interacts with the matrix through covalent and H-bonding, and n-octyltrimethoxysilane (OTMS), a silane that interacts through weak dispersion forces. Interphases with high OTMS mass fractions were found to be fractally rough with fractal dimensions, D(s), between 2.19 and 2.49. This roughness was associated with poor interfacial adhesion and inferior mechanical properties. Mean interparticle distances calculated for composites containing 10 mass % and 25 mass % silica suggest that the nanoparticles treated with more MPTMS than OTMS may be better dispersed than OTMS-rich nanoparticles. The results indicate that the covalent bonding and H-bonding of MPTMS-rich nanoparticles with the matrix are necessary for preparing well-dispersed nanocomposites. In addition, interphases containing equal masses of MPTMS and OTMS may yield composites with overall optimal properties. Finally, the combined SANS/USANS data could distinguish the differences, as a function of silane chemistry, in the nanoparticle/silane and silane/matrix interfaces that affect the overall mechanical properties of the composites.

Dental Materials↗
PubMed2006

Thermal properties and mixing state of ethylene glycol-water binary solutions by calorimetry, large-angle X-ray scattering, and small-angle neutron scattering.

Thermal properties and mixing states of ethylene glycol (EG)-water binary solutions in the entire mole fraction range of EG, 0 < or = x(EG) < or = 1, have been clarified by using differential scanning calorimetry (DSC), large-angle X-ray scattering (LAXS), and small-angle neutron scattering (SANS) techniques. The DSC curves obtained have shown that the EG-water solutions over the range of EG mole fraction 0.3 < or = x(EG) < or = 0.5 are kept in the supercooling state until approximately 100 K, and those in the range of 0.6 < or = x(EG) < or = 0.8 are vitrified, and those in the ranges of 0 < x(EG) < or = 0.2 and 0.9 < or = x(EG) < 1 are crystallized. The radial distribution function (RDF) for pure EG obtained from the LAXS measurements has suggested that a gauche conformation of an EG molecule is favorable in the liquid. The RDFs for the EG-water solutions have shown that the structure of the binary solutions moderately changes from the inherent structure of EG to the tetrahedral-like structure of water when the water content increases. The SANS intensities for deuterated ethylene glycol (HOCD2CD2OH) (EGd4)-water solutions at x(EG) = 0.4 and 0.6 have not been significantly observed in the temperature range from 298 to 173 K, showing that EG and water molecules are homogeneously mixed. On the other hand, the SANS intensities at x(EG) = 0.2 and 0.9 have been strengthened when the temperature decreases due to crystallization of the solutions. On the basis of all the present results, a relation between thermal properties of EG-water binary solutions and their mixing states clarified by the LAXS and SANS measurements has been discussed at the molecular level.

Journal Article↗
PubMed2000

Critical micellization density: A small-angle-scattering structural study of the monomer-aggregate transition of block copolymers in supercritical CO2

In this paper we report a small-angle neutron-scattering investigation of micelle formation by the fluorocarbon-hydrocarbon block copolymer, polyvinyl acetate-b-poly (1,1,2, 2-tetrahydroperfluoro-octyl acrylate) in supercritical CO2 (scCO(2)) at 313 K. At high pressure the copolymer is in a monomeric state with a random coil structure, while at low pressure the polymer forms spherical aggregates stable in a wide range of thermodynamic conditions. By profiling pressure, a sharp monomer-micelle transition is obtained due to the tuning of the solvating ability of scCO(2). We confirm the previous finding that this aggregate-monomer transition is driven by the gradual penetration of CO2 molecules toward the core of the aggregate and is critically related to the density of the solvent, thus giving additional support to the concept of a critical micellization density reported earlier on a similar polymer.

Journal Article↗
PubMed2002

Solution structure of heavy meromyosin by small-angle scattering.

Elucidation of x-ray crystal structures for the S1 subfragment of myosin afforded atomic resolution of the nucleotide and actin binding sites of the enzyme. The structures have led to more detailed hypotheses regarding the mechanisms by which force generation is coupled to ATP hydrolysis. However, the three-dimensional structure of double-headed myosin consisting of two S1 subfragments has not yet been solved. Therefore, to investigate the overall shape and relative orientations of the two heads of myosin, we performed small-angle x-ray and neutron scattering measurements of heavy meromyosin containing all three light chains (LC(1-3)) in solution. The resulting small-angle scattering intensity profiles were best fit by models of the heavy meromyosin head-tail junction in which the angular separation between heads was less than 180 degrees. The S1 heads of the best fit models are not related by an axis of symmetry, and one of the two S1 heads is bent back along the rod. These results provide new information on the structure of the head-tail junction of myosin and indicate that combining scattering measurements with high resolution structural modeling is a feasible approach for investigating myosin head-head interactions in solution.

Animals↗
PubMedDate not supplied

Phenylalanyl-tRNA synthetase from baker's yeast: structural organization of the enzyme and its complex with tRNAPhe as determined by X-ray small-angle scattering.

The quaternary structure of the phenylalanyl-tRNA synthetase and its complex with tRNAPhe was studied in dilute solutions by small angle X-ray scattering. For the free synthetase the radius of gyration was determined as 5.5 nm, the volume 523 nm3, the maximum diameter 17.5 nm and the molecular weight as 260,000 using an isopotential specific volume of 0.735. The overall shape could be best approximated by a flat cylinder with dimensions 18.2 nmx11.5 nmx4nm; the loose structure was approximated by building up the cylinder by spheres (diameter 4.2 nm). The corresponding parameters of the enzyme tRNA complex were the following: radius of gyration 5.9 nm, volume 543 nm3, maximum diameter 21 nm and molecular weight 290,000. These parameters suggest an 1:1 complex, whereby it must be assumed that the tRNA molecule is attached in the extension of the longer axis. From the difference in the distance distribution functions of the free enzyme and the complex it is evident that we have to assume a change of conformation (contraction) of the enzyme upon the binding of the specific tRNA.

Amino Acyl-tRNA Synthetases↗
PubMed1994

A model structure of the muscle protein complex 4Ca2+.troponin C.troponin I derived from small-angle scattering data: implications for regulation.

We report here a model structure for 4Ca2+.troponin C.troponin I derived from small-angle X-ray and neutron scattering data using a Monte Carlo modeling method. In this model, troponin I appears as a spiral structure that wraps around 4Ca2+.troponin C which adopts an extended dumbbell conformation similar to that observed in the crystal structures of troponin C. The troponin I spiral has the approximate dimensions of an alpha-helix and winds through the hydrophobic "cups" in each globular domain of troponin C. The model is consistent with a body of previously published biochemical data on the interactions between troponin C and troponin I, and suggests the molecular mechanism for the Ca(2+)-sensitive switch that regulates the muscle contraction/relaxation cycle involves a signal transmitted via the central spiral region of troponin I.

Amino Acid Sequence↗
PubMed2005

Influence of templating latex on spray dried nanocomposite powders studied by small angle scattering.

Nanoporous powders are prepared in a single step by spray-drying mixtures of small inorganic and larger organic nanoparticles. The structure of these powders has been studied as a function of the mixture's composition using silica and polybromostyrene nanoparticles. Scanning electron microscopy reveals the presence of an increasing concentration of mesopores as the concentration of polybromostyrene increases. By coupling thermogravimetric analysis and ultra-small-angle X-ray scattering, the structure is quantitatively linked to the composition of the porous grains. Experimental USAXS intensities are compared to scattering models for the composite powders. It allows to demonstrate that (i) all mesopores are empty even in the center of the grains, (ii) part of the polymer remains in the micropores of the dried grains. A quantification of the fraction of micropores filled by residual polymer is presented. Such a synthesis procedure can be used to produce hydrophobic porous powders in a one-step process.

Journal Article↗
PubMed1978

[Small-angle scattering of the quaternary structure of phosphofructokinase from baker's yeast].

The phosphofructokinase (E.C. 2.7.1.11) from baker's yeast was examined by means of small angle X-ray scattering in 0.1 M K-phosphate buffer, pH 7. A quaternary structure model was obtained from the comparison of the model scattering curve with the experimental one. The eight subunits of the yeast phosphofructokinase are arranged in a D2-symmetry. The proposed scattering equivalent model corresponds to a structural description with a resolution of 2.5 nm. Models with a C8-symmetry and D4-symmetry can be ruled out.

Macromolecular Substances↗