Fiber Diffraction Patterns Research Articles

Cross-sectional texture of carbon fibres analysed by scanning microbeam X-ray diffraction

Scanning microbeam X-ray diffraction analysis of single carbon fibres allows the cross-sectional orientation distribution (texture) of the carbon layers to be determined, even when the fibre axis is oriented perpendicular to the X-ray beam (fibre geometry). The fibre is scanned across a microbeam with a diameter significantly smaller than the fibre diameter, and fibre diffraction patterns are recorded for every scanning step. The cross-sectional texture information is obtained from the integrated intensities of two different equatorial reflections as a function of the position on the fibre. As an example, results from two different types of carbon fibres are presented: a polyacrylonitrile-based fibre, with random cross-sectional texture, and a fibre based on mesophase pitch, which exhibits a radially folded cross-sectional texture. Detailed modelling of the diffraction data allows a quantitative description of the radial folded texture.

Anomalous thermochromic transition of poly(di‐n‐octylsilane)

AbstractThe thermochromic behavior of poly(di‐n‐octylsilane) {[Si(C8H17)2]n; PDOS} was studied by ultraviolet (UV) absorption, differential scanning calorimetry, and X‐ray diffraction measurements. The structure of PDOS in the low‐temperature phase strongly depended on not only the temperature but also the rate of cooling, that is, the thermal history. Temperature‐dependent UV absorption spectra were highly dependent on thermal hysteresis. Cooled rapidly (10 K/min), PDOS showed two absorption peaks at 3.32 and 3.51 eV in low‐temperature‐ordered phases, whereas a single absorption peak at 3.32 eV became predominant with slow cooling (0.3 K/min). The appearance of the two peaks at low temperatures suggested that a mixture of different conformations was introduced by rapid cooling. A fiber diffraction pattern measured at 240 K after rapid cooling also showed evidence of the existence of novel conformation. A temperature‐dependent powder X‐ray diffraction pattern changed significantly between 270 and 280 K. Rapid cooling reduced the intensity of the X‐ray diffraction peak in this temperature region. This intensity change was explained by the conformational mixture in the polymer. © 2001 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 39: 1085–1092, 2001

Distinct Structural Changes Detected by X-Ray Fiber Diffraction in Stabilization of F-Actin by Lowering pH and Increasing Ionic Strength

Lowering pH or raising salt concentration stabilizes the F-actin structure by increasing the free energy change associated with its polymerization. To understand the F-actin stabilization mechanism, we studied the effect of pH, salt concentration, and cation species on the F-actin structure. X-ray fiber diffraction patterns recorded from highly ordered F-actin sols at high density enabled us to detect minute changes of diffraction intensities and to precisely determine the helical parameters. F-actin in a solution containing 30 mM NaCl at pH 8 was taken as the control. F-actin at pH 8, 30 to 90 mM NaCl or 30 mM KCl showed a helical symmetry of 2.161 subunits per turn of the 1-start helix (12.968 subunits/6 turns). Lowering pH from 8 to 6 or replacing NaCl by LiCl altered the helical symmetry to 2.159 subunits per turn (12.952/6). The diffraction intensity associated with the 27-Å meridional layer-line increased as the pH decreased but decreased as the NaCl concentration increased. None of the solvent conditions tested gave rise to significant changes in the pitch of the left-handed 1-start helix (∼59.8 Å). The present results indicate that the two factors that stabilize F-actin, relatively low pH and high salt concentration, have distinct effects on the F-actin structure. Possible mechanisms will be discussed to understand how F-actin is stabilized under these conditions.

Amyloid fibrils derived from the apolipoprotein A1 Leu174Ser variant contain elements of ordered helical structure.

We recently described a new apolipoprotein A1 variant presenting a Leu174Ser replacement mutation that is associated with a familial form of systemic amyloidosis displaying predominant heart involvement. We have now identified a second unrelated patient with very similar clinical presentation and carrying the identical apolipoprotein A1 mutation. In this new patient the main protein constituent of the amyloid fibrils is the polypeptide derived from the first 93 residues of the protein, the identical fragment to that found in the patient previously described to carry this mutation. The X-ray fiber diffraction pattern obtained from preparations of partially aligned fibrils displays the cross-beta reflections characteristic of all amyloid fibrils. In addition to these cross-beta reflections, other reflections suggest the presence of well-defined coiled-coil helical structure arranged with a defined orientation within the fibrils. In both cases the fibrils contain a trace amount of full-length apolipoprotein A1 with an apparent prevalence of the wild-type species over the variant protein. We have found a ratio of full-length wild-type to mutant protein in plasma HDL of three to one. The polypeptide 1--93 purified from natural fibrils can be solubilized in aqueous solutions containing denaturants, and after removal of denaturants it acquires a monomeric state that, based on CD and NMR studies, has a predominantly random coil structure. The addition of phospholipids to the monomeric form induces the formation of some helical structure, thought most likely to occur at the C-terminal end of the polypeptide.

An X-Ray Diffraction Study on Crystalline and Mesomorphic Structures of Poly(diethylsiloxane)

Crystal structure and molecular packing analysis for crystalline and mesomorphic poly(diethylsiloxane) (PDES) have been studied by wide-angle X-Ray diffraction measurements using uniaxially-oriented PDES sample without crosslinking process. Well-oriented fiber diffraction pattern measured at 0°C, which corresponds to the β2 polymorph, can be satisfactorily indexed by monoclinic unit cell with c (fiber axis)=5.02A. Only four independent reflections can be observed for mesomorphic PDES at 26°C, but the orientational direction of the PDES specimen has been maintained after the crystalline-mesophase transition. Molecular-packing manner of crystalline β2-PDES has been estimated with assuming planar-Si-O-backbone with alternating cis-trans conformation.

The alpha-synucleinopathies: Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy.

Parkinson's disease is the second most common neurodegenerative disease, after Alzheimer's disease. Neuropathologically, it is characterized by the degeneration of populations of nerve cells that develop filamentous inclusions in the form of Lewy bodies and Lewy neurites. Recent work has shown that the filamentous inclusions of Parkinson's disease are made of the protein alpha-synuclein and that rare, familial forms of Parkinson's disease are caused by missense mutations in the alpha-synuclein gene. Besides Parkinson's disease, the filamentous inclusions of two additional neurodegenerative diseases, namely, dementia with Lewy bodies and multiple system atrophy, have also been found to be made of alpha-synuclein. Recombinant alpha-synuclein has been shown to assemble into filaments with similar morphologies to those found in the human diseases and with a cross-beta fiber diffraction pattern. The new work has established the alpha-synucleinopathies as a major class of neurodegenerative disease.

Novel image analysis of two-dimensional X-ray fiber diffraction patterns: example of a polypropylene fiber drawing study

On-line studies of the structural development during continuous drawing of a polypropylene fiber were carried out using synchrotron wide-angle X-ray diffraction. A unique image analysis method was introduced to extract quantitative information on the crystal, amorphous and mesomorphic fractions. In addition, the unit-cell parameters and the crystal orientation were obtained under various draw conditions. It was found that the mesophase remained about constant during drawing. At draw ratios less than 6.0, the crystallinity increased and the crystal density decreased as a result of the stress-induced crystallization of crystals with a large degree of disordering. At draw ratios above 6.0, the crystallinity increased slowly and the decrease in crystal density was also retarded because of the draw-induced melting. The crystal orientation increased with increasing draw ratio up to a ratio of 6.0 and then decreased, probably because of chain breakage.

The likelihood function in fiber diffraction

The likelihood function is an appropriate target function for refinement of molecular structures using fiber diffraction data. However, its practical application to fiber diffraction faces two significant obstacles: (i) the intensities of layer lines in a fiber diffraction pattern usually arise from the superposition of several terms, each equivalent to a crystallographic structure factor, thereby making the calculation significantly more complex than for the crystallographic case; (ii) to describe a molecular structure at the atomic level based on fiber diffraction data, the radial and phase parts of the atomic coordinates must be treated separately owing to the uniaxial symmetry of the structure. These issues are addressed here in order to derive equations of likelihood functions for fiber diffraction. The special case of a single term on a layer line is treated first followed by extension of the method to the multiterm case. A practical difficulty in implementation of likelihood for the multiterm case is that each term has a different variance. An analytical technique is described that allows the conversion of the unequal-variance case to an equal-variance case. This makes it possible to express the likelihood by an explicit formula, allowing a direct implementation of the likelihood calculation. A cylindrically symmetric model is proposed for error distribution of the atomic coordinates in a helical structure. Variances and offset coefficients of the contributing terms in the likelihood functions are expressed in terms of the variance of the atomic coordinates in the cylindrical reference system.

Glycosaminoglycan conformation: do aqueous molecular dynamics simulations agree with x-ray fiber diffraction?

Glycosaminoglycan-protein interactions are biologically important and require an appreciation of glycan molecular shape in solution, which is presently unavailable. In previous studies we found strong similarity between aqueous molecular dynamics (MD) simulations and published x-ray diffraction refinements of hyaluronan. We have applied a similar approach here to chondroitin and dermatan, attempting to clarify some of the issues raised by the x-ray diffraction literature relating to chondroitin and dermatan sulfate. We predict that chondroitin has the same beta(1-->4) linkage conformation as hyaluronan, and that their average beta(1-->3) conformations differ. This is explained by changes in hydrogen-bonding across this linkage, resulting from its axial hydroxyl, causing a different sampling of left-handed helices in chondroitin (2.5- to 3.5-fold) as compared with hyaluronan (3.0- to 4.0-fold). Few right-handed helices, which lack intramolecular hydrogen-bonds, were sampled during our MD simulations. Thus, we propose that the 8-fold helix observed in chondroitin-6-sulfate, represented in the literature as an 8(3) helix (right-handed), though it has never been refined, is more likely to be 8(5) (left-handed) helix. Molecular dynamics simulations implied that (4)C(1) and (2)S(O), but not (1)C(4), forms of iduronate could be used in refinements of dermatan x-ray fiber diffraction patterns. Current models of 8-fold dermatan sulfate chains containing (4)C(1) iduronate refine to right-handed helices, which possess no intramolecular hydrogen-bonds. However, MD simulations predict that models containing (2)S(O) iduronate could provide better (8(5) helix) starting structures for refinement. Thus, the 8-fold dermatan sulfate refinement (8(3) helix) could be in error.

Fibre Diffraction Using the BioCAT Facility at the Advanced Photon Source

The BioCAT undulator-based beamline at the Advanced Photon Source (APS), Argonne IL, USA is a state-of-the-art instrument for biological noncrystalline diffraction and X-ray absorption spectroscopy that is generally available to the international scientific community. The design features of this instrument and the unique source properties of the APS allow collection of fibre diffraction patterns of exceptional quality from complex, weakly diffracting biological systems. The small focal spots achievable with this instrument (~40 x 200 microns) has allowed excellent discrimination of fine detail in fibre patterns from muscle and connective tissue as well as detection of weak diffraction features in the presence of large backgrounds. The high X-ray flux of the instrument (~1.5 x 1013 photons/s at 12 keV) permits dynamical experiments on these systems with very fast time resolution. Letters 475, 11-16. [17] Boehm, M. K., Woof, J. M., Kerr, M. A., Perkins, S. J. (1999) J. Mol. Biol. 286, 1421-1447. [18] Aslam, M., Perkins, S. J. (2001) Submitted.

CPRL: a program to plot the cylindrically projected reciprocal lattice for fiber diffraction patterns

The positions of reflections on the diffraction pattern from a polycrystalline fiber are described by a cylindrical projection of the reciprocal lattice. The characteristics of the projection depend on the crystal system and the orientation of the fiber axis relative to the unit-cell axes. The programCPRLplots the positions of the reflections on a diffraction pattern from an oriented polycrystalline fiber (the cylindrically projected reciprocal lattice), for a triclinic unit cell with any orientation of the fiber axis. The results provided by the program facilitate interpretation of fiber diffraction patterns for complex systems.

The molecular conformations of polytetrafluoroethylene: forms II and IV

The crystal structure of polytetrafluoroethylene, –(CF2)n–, is unusual in having a number of crystal forms and also possessing substantial molecular motion within the crystal well below the melting point. This article deals with the unusual first-order transition occurring at about 19°C, changing the crystal structure from form II to form I. This article also updates current literature on the crystal structures of these two forms. X-ray and electron diffraction data from forms II and IV are interpreted as helical structures. Form II is defined mathematically as a non-commensurable helix close to a 13/6 conformation of six turns per 13 (CF2) groups. Form IV is interpreted as a commensurable 15/7 helix which is consistent with space group P31. Fiber diffraction patterns of these forms are described in detail.

Aspects of X-ray diffraction on single spider fibers

Diffraction patterns of silk from several spider species have been obtained by synchrotron radiation using a beam size ≥10 μm. Single fiber diffraction patterns were obtained for fiber diameters down to a few microns. Diffraction patterns recorded with a 10 μm wide X-ray beam displayed fiber texture. The presence of two fractions of different crystallinity was confirmed for a single Nephila clavipes fiber. The orientation distribution of the polymer chains of the crystalline fraction along the fiber axis was found to be about 23° full-width at half maximum (fwhm). The azimuthal spread of the short-range order fraction was about 86° fwhm.

Analysis of X-ray diffraction from fibres of pf1 Inovirus (filamentous bacteriophage) shows that the DNA in the virion is not highly ordered

X-ray fibre diffraction patterns of well-aligned Pf1 filamentous bacteriophage show sharp layer-lines attributable to an ordered helical array of protein subunits. Electron density maps calculated from the intensity on these layer-lines show no evidence for DNA following the symmetry of the protein, nor is there evidence on the diffraction patterns for the additional layer-lines expected if ordered DNA follows a symmetry different from that of the protein. We conclude that the interactions between DNA and protein in the Pf1 virion, like those in the Ff virion, are delocalized rather than specific, and the DNA structure in the virion is less regular than the protein structure. This conclusion has implications for the process of virion assembly, and we suggest a possible model for the change in the viral DNA symmetry as the DNA is passed to the virion from the intracellular complex with the viral gene 5 single-stranded DNA-binding protein.

Iterative Low-Pass Filtering for Estimation of the Background in Fiber Diffraction Patterns

Disorientation of particles in fibrous specimens results in diffraction patterns in which the layer-line intensity is arced about the center, causing layer lines to overlap at larger radii and, as a consequence, making correction of the background problematic. Taking advantage of the fact that the background is typically made up of spatial frequencies that are substantially lower than those constituting the diffracted intensities, estimates of background in fiber diffraction patterns were made by applying an iterative low-pass filter to the diffraction data. This procedure has been applied to X-ray fiber diffraction patterns from filamentous bacteriophages to calculate the intensities along layer lines as well as to correct for the background.

Fiber diffraction patterns for general unit cells: the cylindrically projected reciprocal lattice

The positions of reflections on the diffraction pattern from a polycrystalline fiber are described by a cylindrical projection of the reciprocal lattice. The characteristics of the projection depend on the crystal system and the orientation of the fiber axis relative to the unit-cell axes. Expressions describing the cylindrically projected reciprocal lattice for a general triclinic system and any orientation of the fiber axis are derived. Calculations using these expressions illustrate characteristics of the projected reciprocal lattice and aid in the interpretation of fiber diffraction patterns.

WAXS analysis of structural changes of poly(ethylene terephthalate) fibers induced by supercritical-fluid dyeing

Supercritical CO2 fluid, a new environmentally friendly dyeing medium, changes the fiber structure to a certain extent in dependence on the treatment temperature and pressure used. Therefore the changes of crystalline structure in poly(ethylene tereph-thalate) (PET) fibers as brought about under the influence of supercritical CO2 fluid were investigated. For the data collection of wide-angle X-ray diffraction full patterns a two-circle goniometer, equipped with a position sensitive detector, was used. From the observed two-dimensional fiber diffraction patterns the crystallinities of various treated fibers were evaluated. The equatorial scanning yielded the dimensions of crystallites. To elucidate the fiber-surface morphology changes SEM analyses were performed. The supercritical fluid dyeing of PET fibers with highly developed microfibrillar structure under taut-ends conditions promotes changes which are characterized by an increase in crystallinity and by diminution of the apparent crystallite dimensions. Some changes of surface morphology of dyed fibers were observed as well.

Application of a CCD-based X-ray diffractometerto polymer fibre diffraction

A new diffractometer has been built incorporating a small-area charge-coupled device (CCD) as the X-ray detector. The diffractometer is suitable for studying uniaxially oriented polymer fibres, and produces high resolution fibre diffraction data considerably faster than is possible using a conventional scintillation counter. The sample and detector are mounted on a 3-circle goniometer, and a fibre pattern is constructed from a series of separate diffraction ‘snapshots’, each centred on a different point in reciprocal space. The advantages of the new system are the ability: (1) to produce an undistorted representation of the fibre diffraction pattern; and (2) to access reflections close to the reciprocal fibre axis which are often missing from normal incidence X-ray fibre diffraction photographs. These features make it particularly useful for studying diffuse scattering from partially ordered materials. The operation of the diffractometer is demonstrated using fibres of polyethylene, polypropylene and a copolymer of 1.4-hydroxybenzoic acid with 2,6-hydroxynaphthoic acid. In the latter case a detailed examination of the shapes of the meridional reflection is possible, demonstrating them to be consistent with predictions from current crystallization theories. The effect of imperfect molecular orientation on the appearance of the fibre diffraction patterns is also discussed.

Determination of Peptide Amide Configuration in a Model Amyloid Fibril by Solid-State NMR

The ‚-amyloid proteins (A‚), especially the variant A‚1-42, are the primary constituent of the amyloid plaques which are characteristic of Alzheimer's disease (AD). The C-terminus of A ‚ has been identified as crucial for rapid amyloid formation. A 9-residue C-terminal fragment of A‚ (designated ‚34-42, with sequence LMVGGVVIA) forms a structured aggregate which is classified as an amyloid fibril based primarily on its morphological and solubility properties and the classic cross- ‚ fiber diffraction pattern it displays. We have adopted this aggregate as a model of the A‚-dominated amyloid plaques associated with AD. Previous results from a series of internuclear 13 C- 13 C distance measurements along the peptide backbone indicate that the ‚34-42 backbone conformation differs considerably from that of the classic ‚-sheet, possibly including an unusual cis amide bond in the peptide's central glycyl -glycyl region. Here we report evidence which demonstrates the presence of a trans configuration at the peptide linkage between these residues. The evidence derives from solid-state NMR static echo and n ) 2 rotational resonance experiments which probe the orientation of the 13 C carbonyl chemical shift anisotropy (CSA) tensor of the peptide bond with respect to the dipolar tensor connecting the carbonyl carbon to the 13 C-

Common core structure of amyloid fibrils by synchrotron X-ray diffraction

Tissue deposition of normally soluble proteins as insoluble amyloid fibrils is associated with serious diseases including the systemic amyloidoses, maturity onset diabetes, Alzheimer’s disease and transmissible spongiform encephalopathy. Although the precursor proteins in different diseases do not share sequence homology or related native structure, the morphology and properties of all amyloid fibrils are remarkably similar. Using intense synchrotron sources we observed that six different ex vivo amyloid fibrils and two synthetic fibril preparations all gave similar high-resolution X-ray fibre diffraction patterns, consistent with a helical array of β-sheets parallel to the fibre long axis, with the strands perpendicular to this axis. This confirms that amyloid fibrils comprise a structural superfamily and share a common protofilament substructure, irrespective of the nature of their precursor proteins.