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Assemblies of Alzheimer’s peptides Aβ25–35 and Aβ31–35: reverse-turn conformation and side-chain interactions revealed by X-ray diffraction

Alzheimer’s β amyloid protein (Aβ) is a 39 to 43 amino acid peptide that is a major component in the neuritic plaques of Alzheimer’s disease (AD). The assemblies constituted from residues 25–35 (Aβ25–35), which is a sequence homologous to the tachykinin or neurokinin class of neuropeptides, are neurotoxic. We used X-ray diffraction and electron microscopy to investigate the structure of the assemblies formed by Aβ25–35 peptides and of various length sequences therein, and of tachykinin-like analogues. Most solubilized peptides after subsequent drying produced diffraction patterns characteristic of β-sheet structure. Moreover, the peptides Aβ31–35 (Ile–Ile–Gly–Leu–Met) and tachykinin analogue Aβ(Phe 31)31–35 (Phe–Ile–Gly–Leu–Met) gave powder diffraction patterns to 2.8 Å Bragg spacing. The observed reflections were indexed by an orthogonal unit cell having dimensions of a=9.36 Å, b=15.83 Å, and c=20.10 Å for the native Aβ31–35 peptide, and a=9.46 Å, b=16.22 Å, and c=11.06 Å for the peptide having the Ile31Phe substitution. The initial model was a β strand where the hydrogen bonding, chain, and intersheet directions were placed along the a, b, and c axes. An atomic model was fit to the electron density distribution, and subsequent refinement resulted in R factors of 0.27 and 0.26, respectively. Both peptides showed a reverse turn at Gly33 which results in intramolecular hydrogen bonding between the antiparallel chains. Based on previous reports that antagonists for the tachykinin substance P require a reverse turn, and that Aβ is cytotoxic when it is oligomeric or fibrillar, we propose that the tachykinin-like Aβ31–35 domain is a turn exposed at the Aβ oligomer surface where it could interact with the ligand-binding site of the tachykinin G-protein-coupled receptor.

Structure of synthetic 6-line ferrihydrite by electron nanodiffraction

Single-crystal electron diffraction patterns of nanocrystals in two samples of synthetic six-line ferrihydrite (6LFh) were obtained using electron nanodiffraction to produce diffraction patterns from areas between ~0.7 and 5 nm across. One of the samples was synthesized at 75 °C by a conventional method; the other was synthesized by a recently developed room-temperature technique. Structures of individual nanocrystals were investigated by comparing experimental and simulated electron-diffraction patterns. The most common structure in each sample is based on double-hexagonal (ABAC) stacking of close-packed oxygen layers, and is similar to the “defect-free ferrihydrite” structure proposed by Drits and co-workers. Nanocrystals with maghemite- or magnetite-like structures and structures similar to those in two-line ferrihydrite (2LFh) occur less commonly in both samples. The sample synthesized at room temperature has a small amount of hematite, which was not found in nanodiffraction patterns from the 75 °C sample. The most common structure in 6LFh is distinct from those previously determined by nanodiffraction of 2LFh, indicating that 6LFh is not simply a more crystalline form of 2LFh.

Structure of synthetic 2-line ferrihydrite by electron nanodiffraction

Comparison of experimental single-crystal electron diffraction patterns of synthetic two-line ferrihydrite (2LFh) with simulated single-crystal electron-diffraction patterns indicates that a synthetic 2LFh sample contains highly disordered material and nanocrystals with structures based on hexagonal (ABAB) and cubic (ABC) stacking of close-packed layers of O 2 - and OH- ions. An apparently continuous variation in ordering exists between the highly disordered material and each of the crystalline structures, suggesting that both nanocrystalline structures represent local extremes of three-dimensional ordering. Experimental diffraction patterns were obtained using electron nanodiffraction, a technique in which the finely focused beam from a field-emission gun in an electron microscope can be used to produce diffraction patterns from areas <1 nm across. Nanodiffraction patterns from the highly disordered material have diffuse streaks rather than distinct reflections, and are consistent with a two-dimensional structure that consists of close-packed anionic layers with essentially complete stacking disorder and nearly random distribution of Fe atoms. The structure with cubic stacking is similar to maghemite and has ~25% of the Fe in tetrahedral sites. The structure with hexagonal stacking consists of double chains of face-sharing Fe octahedra; each octahedron shares one face, two edges, and three corners with adjacent octahedra. Previous results from transmission electron microscopy, powder X-ray and electron diffraction, and synchrotron-based techniques reflect the overall high degree of structural disorder rather than the characteristics of the maghemite-like and double-chain structures

Scattering from groove patterns in a perfectly conducting surface

Electromagnetic scattering is investigated for assemblages of parallel open cavities recessed in a perfectly conducting ground plane. Cavities of a variety of shapes are treated, with cross-sectional dimensions of the order of one or two electromagnetic wavelengths. Under the assumption that the cavities form grooves of effectively infinite length, a two-dimensional analysis treats transverse incidence under both E- and H-polarized illumination (E and H fields parallel to groove axis, respectively). For the most part, any coupling between cavity responses on the surface produces negligible effects on far-field diffraction patterns, even when cavities are extremely close together and when induced currents flow between adjacent cavities. Thus one may usually construct diffraction patterns for assemblages of grooves by simply superposing responses calculated for each cavity in isolation. Despite possibly substantial differences among the individual scattering patterns from contributing cavities, regularly spaced arrangements of two or more cavities produced grating-type diffraction patterns. This allows inference of the distance between grooves, based on separation between the pattern’s peaks and troughs. Combinations of dissimilar cavities may produce diffraction patterns with peaks that are shifted away from locations expected on the basis of the grating equation, but with a characteristic spacing between the peaks approximately preserved. Random perturbation of groove locations relative to uniform spacing produces a decay in ensemble-average diffraction pattern as scattering angles diverge from the specular direction. A simple theory quantifies the exponential dependency of this grating pattern suppression and shows its effect on the angular range available for identification of scattering characteristics. Monte Carlo–type backscatter simulations including all intercavity coupling demonstrate the success of the theory and thereby explain the type of pattern suppression seen in measurements.

The Structure of Amyloid Fibrils by Electron Microscopy and X-Ray Diffraction

Publisher Summary The chapter discusses the structural analysis of amyloid fibrils by electron microscopy and X-ray diffraction. A method to isolate amyloid fibrils from tissue was developed, and such preparations of purified fibrils exhibited the classic staining and birefringent characteristics of crude amyloid samples. The further use of high-resolution electron microscopy, examining ultrathin sections of tissue and isolated material, confirmed the fibrillar form as the characteristic appearance of amyloid in the electron microscope. With the ability to prepare samples of isolated amyloid fibrils it began to be possible to probe the molecular structure of the fibrils using X-ray diffraction. The initial use of this technique produced diffraction patterns that showed that the fibrils were composed of polypeptide chains, extended in the so-called cross-β-conformation. Subsequent analyses by X-ray diffraction on a variety of amyloids and also by NMR analysis have confirmed that the protein chains in all amyloid fibrils are predominantly in the cross-β-conformation. The structures of the soluble, globular forms of several amyloidogenic proteins have been determined by the single crystal X-ray crystallography. The origins of the different amyloidoses appear quite diverse, with some arising from a genetic mutation and others apparently from polypeptide misprocessing or from an unusual accumulation of full-length wild-type protein.

Growth rate dispersion in small crystals and its relation to mosaic spread

High mosaic spread is a common feature of a number of complex materials (such as certain zeolites and protiens) for which the preparation of large single crystals is prohibited. In one previous systematic study, a direct correlation between growth rate and mosaic spread was found for very small crystals of sodium chlorate. This work has attempted to explore the generality of the effect by extending measurements to a wider range of simple materials. Small crystals (5–200 μm) of ammonium dihydrogen phosphate (ADP), sodium chlorate and sucrose, generated by secondary nucleation in aqueous solution, have been grown under constant conditions of supersaturation. A wide dispersion of growth rates was observed for each material using optical microscopy. A number of individual crystals of known growth rate were successfully retrieved from solution and an assessment of the mosaic spread of each crystal was made using synchroton radiation Laue diffraction at Daresbury Laboratory. All of the crystals produced diffraction patterns comprising small, sharp spots, indicative of low mosaic spread ( <0.5°). No correlation was found between growth rate and mosaic spread for these relatively simple structures. In addition, individual crystals of sucrose have also been examined immediately after creation in solution and subsequently grown-on at constant supersaturation. The Laue patterns obtained for each crystal, both before and after growth, exhibited low mosaic spread, yet each crystal grew at different rate. It is suggested that radiation damage can account for the previously published discrepancies, and acceptable radiation doses are calculated for the determination of mosaic spread in these materials.

Laser diffraction determination of the crystalline structure of an electrorheological fluid.

The electric-field-induced structures of small glass spheres in silicone oil produce laser diffraction patterns which verify, for the first time, the body-centered-tetragonal lattice structure predicted by theory. By a mechanism totally unlike that of conventional x-ray scattering, the incident laser beam propagates through the lattice of close-packed spheres via stable optic modes along regular arrays of transparent spheres, and then produces diffraction patterns after exiting from the lattice.

Structure of Na overlayers on Ru(0001) at room temperature and above

The adsorption of sodium on the Ru(0001) surface at 300 K and above has been studied by LEED, Auger spectroscopy, thermal desorption and work function measurements. A new high temperature peak observed in the thermal desorption spectra was identified as due to the desorption of ions occurring at very low coverages. In the high coverage range new LEED patterns were observed corresponding to the formation of ordered first and second layers of sodium. Models of “non-planar” commensurate structures ( 2 3 × 2 3 )R30° for the first adlayer and ( 4 3 × 4 3 ) for the second are proposed. A reversible change in the LEED patterns was found to occur at T = 600 K. This effect is explained as a result of the existence of two types of binding states in the first layer due to the three- and six-fold symmetry sites on the substrate. The sodium atoms in those states may be considered as two separate components and, thermally activated, produce diffraction patterns as if they belonged to two different layers.

Anisotropic packing and diffraction-peak shifts in icosahedral glasses.

We show that the anisotropic random packing of units with icosahedral symmetry produces diffraction patterns with distortions similar to recent electron and x-ray diffraction measurements. Using the Hendricks-Teller formalism discussed in an earlier paper, we show that the peak shifts predicted by the introduction of phason strain in an ideal quasilattice may also be described by this anisotropic, random-packing, icosahedral glass model.

Electron diffraction experiments on argon clusters nucleated in helium using Laval nozzle beams

A cluster beam-electron diffraction machine has been modified with a low-temperature ( T 0 = 100 K), Laval nozzle source to nucleate noble gases as a small mole fraction (χ 0 to 0.01) in helium carrier gas. The use of specific nozzle contours, plus the variables above, allows one to nucleate clusters which have as narrow a size distribution as possible and which are colder (10 K) than clusters formed in pure-gas expansions. These features simplify, in principle, the interpretation of diffraction patterns and tend to form cluster structures which are in minimum-energy configurations. Electron diffraction experiments are carried out on argon clusters and show a transition from fcc to a non-crystalline structure over the size range from 3500 to 1500 atoms per cluster. A relaxed icosahedral cluster model produces diffraction patterns consistent with the experiments. Model diffraction patterns reveal that the height of the knee on the (111) peak is an excellent parameter for the size determination of icosahedral clusters.

MEED study of some crystalline surfaces

A new medium energy electron diffraction (MEED) system, which can observe both back scattering (BSMEED) and forward scattering (RMEED) patterns from the same surface of crystalline solids has been designed. Results obtained from MgO(001) and GaAs(001) indicate that MEED has the following favourable characteristics: (1) Unlike LEED, post-acceleration of the diffracted beam with a grid is not necessary for MEED. The diffraction pattern can be seen directly on a fluorescent screen. (2) Collimation and focusing of the incident beam are readily achieved and sharp diffraction spots are observed. (3) Unlike RHEED, a strictly flat surface is not necessary for MEED. Relatively rough, but clean surfaces can produce diffraction patterns. (4) From Kikuchi lines or bands it is possible to determine the precise orientation of the crystal surface. (5) By changing the energy of the incident beam it is possible to observe the surface layer both in two and three dimensions.

Characterization of fiber orientation in short-fiber composites

A method for measuring intermediate states of fiber orientation in short-fiber composites is described. The technique is based on the observation that a representative fiber distribution, for example, the negative of a photomicrograph from a specimen, resembles a collection of diffraction apertures. Diffraction masks for a Fraunhofer diffractometer made from the representative fiber distributions produce diffraction patterns characteristic of the state of orientation. Analyses are presented which relate the features of the diffraction pattern to (i) the orientation distribution, (ii) shape, and (iii) aspect ratio of the fibers. The results from these analyses are in good agreement with experimental diffraction patterns from masks made from simulated fiber distribution patterns.

Centro-symmetry in Fraunhofer Diffraction Patterns

Most of the known Fraunhofer diffraction patterns are centro-symmetrical. The cause of this symmetry is usually a real object transmittance, but complex objects with phase factors can also cause diffraction patterns with centro-symmetry. Actually, the set of real objects is only a small sub-set of the set of all those objects that produce diffraction patterns with centro-symmetry.

The approximation of asymmetric neutron powder diffraction peaks by sums of Gaussians

Neutron powder diffractometers operating with large vertical counter acceptance angles produce diffraction patterns in which the peaks are shifted and broadened, and may become distinctly asymmetric. It is shown that a sum of Gaussians generally provides a good approximation to these peaks. The sum of Gaussians has been included as an optional description of the profile within an existing profile refinement program. In this application, the sum incorporates a single asymmetry parameter which can be estimated from the diffractometer geometry or determined in the refinement. It is recommended that, in describing asymmetric peaks, the sum of Gaussians be used in place of the simple Gaussian multiplied by Rietveld's semi-empirical asymmetry factor.

Structural study of cellophane

Fine structural aspects of cellophane have been investigated using X-ray and electron diffraction techniques as well as a kinetic study of the dissolution of cellophane in 0.5 M cupriethylene diamine solution. The X-ray diffraction pattern for cellophane shows a typical cellulose II structure while the electron diffraction pattern highlights a typical cellulose I structure with very weak reflection for a cellulose II type lattice. The kinetics study of cellophane dissolution in cupriethylene diamine confirms the presence of these polymorphic forms of cellulose in cellophane. The paper also reports studies of the X-ray and electron diffraction patterns of cellophane in relation to crystallite size and degradation under electron beam. It is shown that the observed anomaly between the X-ray and electron diffraction patterns of cellophane is a consequence of (i) the larger minimum crystallite size requirement for producing diffraction patterns with X-rays than with the electron beam (ii) the much faster degradation of cellulose II crystallites than that of cellulose I crystallites under the electron beam and (iii) the reduction in the crystallite size of cellulose II in cellophane from that in wood pulp alkali cellulose during the process of regeneration.

Structural characterization of ordered domains in a hydrophobic membrane protein

AbstractA delipidized proteolipid protein fraction was purified from organic solvent extracts of bovine cerebral cortex and studied by means of diffraction, electron microscopic, and ir techniques. Special use was made of an electron diffraction procedure which minimized the electron damage to the biological specimens. The ir spectroscopy of the apoprotein fraction indicated the presence of polypeptides in extended β‐conformation, possibly in the antiparallel mode of packing. Electron microscopy of the fraction, negatively stained in organic media, made apparent the presence of both ordered and amorphous material. Only the former, characterized by repeating units of about 40–45 Å in diameter and varying length, produced diffraction patterns in the selected area mode exhibiting a highly undistorted lattice. The two‐dimensional cell parameters of the protein fraction were a = 4.79 Å, b = 7.20 Å, and γ = 90°. The plane group symmetry, corresponding to the systematic absences, was p 2gg, consistent with the β‐pleated sheet structure of simple polypeptides.

Small angle X-ray scattering from the inner and outer membranes from Escherichia coli

Small angle X-ray data from purified forms of inner or cytoplasmic and outer membranes from Escherichia coli have been obtained and appear to be qualitatively similar. Transitory changes are apparent in the circularly averaged X-ray profiles from inner membrane. Such results could be due to the loss or denaturation of peripheral membrane proteins. Some partially dried forms of outer membrane are partly ordered and produce diffraction patterns which support an underlying bilayer structure. An extra light membrane fraction which results from membrane preparations utilizing a French pressure cell for spheroplast disruption has been characterized and shown to be similar to inner membrane. The purified membranes produce small angle X-ray diffraction patterns which are much different from those of lipid dispersions and the differences are attributable to the high protein content of the intact membranes. While the small angle X-ray region may be useful for characterizing the membrane preparations, the paucity of detail in the diffraction pattern suggest that it will be of little value in describing the complex underlying membrane structure.

A versatile automatic X-ray diffractometer for the study of high vapour pressure liquids

An automatic, horizontal axis X-ray diffractometer is described employing Bragg-Brentano para-focusing geometry, with post diffraction monochromatization. The diffractometer is specially designed to examine either the top free surface or, in the present work, the lower surface of a liquid. The lower surface is irradiated through a beryllium window in the base of a cell. Measurements on liquid mercury at 23 degrees C indicate that the technique produces diffraction patterns in good agreement with those of other workers.

The diffraction of satellite signals by isolated ionospheric irregularities

Procedures are given for the rapid calculation of refraction and diffraction patterns produced by isolated ionospheric irregularities. These patterns are observed experimentally, and a sensitive polarisation angle recorder is also used to determine the associated changes in electron content. Large scale irregularities in the F-region are shown to cause variations of several decibels in the amplitude of 20 and 40 MHz satellite signals. Dense, isolated irregularities produce patches of ‘scintillations’ on 20 MHz. The common assumption that scintillations are caused by a large number of small irregularities, acting as a random diffracting screen, is therefore incorrect on many occasions. Small isolated irregularities produce diffraction patterns which depend only on the total number of electrons in the irregularity, and the height. Irregularities of all sizes commonly occur in trains; in such cases the height of the irregularities can be determined by comparing the depth of the fluctuations in amplitude and in polarisation. Calculated heights are mostly in or above the F-region. For large isolated irregularities, their position with respect to the peak of the F-layer can be obtained directly from the different times at which amplitude fluctuations occur on 20 and 40 MHz.

Structure of Amorphous Alloy Films

Amorphous films are understood to be solids in which the postulated atomic arrangement shows no crystallike ordering beyond a few neighbors. The structure of such amorphous films is usually characterized by a diffuse x-ray or electron-diffraction pattern, consisting of a few broad rings or halos, and by a lack of contrast in transmission electron micrographs. However, very small, randomly oriented crystallites of <30 Å in diameter will also produce diffraction patterns which are qualitatively similar to those exhibited by amorphous solids. The theories of small-angle scattering and large-angle diffraction are discussed in terms of the structural disorder in the solids (electron-density fluctuations, atomic distributions, particle sizes) and are applied to the investigations of the structure of amorphous alloy films, such as liquid-quenched Fe–P–C and Pd–Si alloys, electrodeposited Ni–P alloys, and vapor-quenched Cu–Mg and Ag–Cu alloys.