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Development, structure, and function of the nail
Published in Eckart Haneke, Histopathology of the NailOnychopathology, 2017
Fiber diffraction using special X-ray sources or small angle X-ray beam-lines at synchrotones are said to give specific diffraction patterns allowing the diagnosis of cancers and melanoma to be made from nail samples.222
X-Ray Diffraction as a Tool for Studying Collagen Structure
Published in Marcel E. Nimni, Collagen, 1988
Barbara Brodsky, Shizuko Tanaka, Eric F. Eikenberry
A large amount of diffuse equatorial scattering is always observed in X-ray diffraction patterns of connective tissues. In tissues with noncrystalline fibrils, this is the dominant equatorial scatter, while in crystalline fibrils, it constitutes a background to the discrete reflections. Such diffuse scatter indicates lateral disorder of the molecules, but since X-ray data are collected over relatively long time periods of at least 1 day, this disorder could be static (i.e., due to the presence of a number of fixed conformations) or dynamic (i.e., due to motion of the molecules). These different kinds of disorder can be distinguished by recording X-ray patterns at low temperatures, since the dynamic disorder, but not static disorder, would be expected to decrease with temperature. Recently, protein crystallographers have begun such low temperature studies and have interpreted their structural results in terms of protein dynamics.43 Such analyses are theoretically possible for fiber diffraction as well, and could then be correlated with experimental results from13 C nuclear magnetic resonance7 and other methods that detect significant mobility in collagen fibrils.
Order Tubulavirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
Zeri et al. (2003) determined the structure of the fd coat in solution by solid-state NMR spectroscopy. This structure that is shown in Figure 11.3 differed from that previously determined by x-ray fiber diffraction. Most notably, the 50-residue protein was not a single curved helix but rather was a nearly ideal straight helix between residues 7 and 38, where there was a distinct kink, and then a straight helix with a different orientation between residues 39 and 49. Residues 1–5 have been shown to be mobile and unstructured, and proline 6 terminated the helix (Zeri et al. 2003). Marvin et al. (2006) reinterpreted the NMR data and showed their consistency with the model derived from the x-ray fibre diffraction studies. In parallel, Wang YA et al. (2006) reported the first image reconstruction of the phage fd by electron cryomicroscopy. Although the thin rather featureless filaments scattered weakly, the authors achieved a nominal resolution of ∼8 Å using an iterative helical reconstruction procedure. The two different conformations of the virus were found, and in both states the subunits were packed differently than in conflicting models previously proposed on the basis of x-ray fiber diffraction or solid-state NMR studies. A significant fraction of the population of wild-type fd was either disordered or in multiple conformational states, while in the presence of the Y21M mutation this heterogeneity was greatly reduced (Wang YA et al. 2006). Moreover, the refined electron microscopy model of the phage fd closely approximated the model derived directly from x-ray fiber diffraction and solid-state NMR data (Straus et al. 2008b). The consensus structure of the x-ray and solid-state NMR data was published also for the phage Pf1 (Straus et al. 2008a, 2011). Xu J et al. (2019) resolved the structure of the phage IKe to 3.4 Å, providing therefore atomic details on the structure of the major coat protein, the symmetry of the capsid shell, and the key interactions driving its assembly. Remarkably, the phage IKe was selected for the development of the advanced 4D solid-state NMR technique (Porat et al. 2021).
Emerging drugs for the treatment of light chain amyloidosis
Published in Expert Opinion on Emerging Drugs, 2020
Rajshekhar Chakraborty, Suzanne Lentzsch
Systemic immunoglobulin light chain amyloidosis [AL Amyloidosis] is a disorder of protein misfolding that is characterized by the deposition of fibrillar protein aggregates derived from immunoglobulin light chains. The amyloidogenic protein [i.e. light chain] typically circulates in the blood and deposits as highly organized protein fibrils in one or more target organs [1]. The protein deposits in amyloidosis are characterized by cross-β fiber diffraction pattern on X-rays and apple-green birefringence on Congo red staining under polarized light [1–3]. The amyloidogenic protein originates from monoclonal plasma cells in the bone marrow that produces kinetically unstable light chain due to somatic mutations in the light chain variable region [4–6]. This further leads to misfolding and improper aggregation of light chain, which, together with interaction with the microenvironment, leads to initial nucleation of deposits and oligomer formation. The oligomers serve as a template that eventually helps in the formation of highly organized amyloid fibrils and leads to end organ damage by physical replacement of tissue parenchyma as well as direct cytotoxicity from amyloid deposits [3].
Flagellin as a vaccine adjuvant
Published in Expert Review of Vaccines, 2018
Baofeng Cui, Xinsheng Liu, Yuzhen Fang, Peng Zhou, Yongguang Zhang, Yonglu Wang
Previous studies on the structure of flagellin by electron cryomicroscopy and X-ray fiber diffraction at approximately 10 Å resolution revealed that identical structural units of single flagellin linked by non-covalent bonds assemble the helical filament and are responsible for the polymorphism of filaments [22–27]. However, much higher resolution provided us novel insights into the special structural basis of supercoiling at sub-angstrom precision [28,29]. In their construction model, the complete flagellin structure can be divided into four domains, labeled D0, D1, D2, and D3. These domains are arranged from the inside to the outside of the filament. The N-terminal chain starts from D0, passes through D1 and D2, reaches D3, and then returns through D2 and D1; the C-terminal chain ends at D0. Thus, the overall shape of flagellin viewed perpendicular to the filament axis appears as an upper-case Greek gamma (Γ).
Full-length TDP-43 and its C-terminal domain form filaments in vitro having non-amyloid properties
Published in Amyloid, 2021
Claudia Capitini, Giulia Fani, Mirella Vivoli Vega, Amanda Penco, Claudio Canale, Lisa D. Cabrita, Martino Calamai, John Christodoulou, Annalisa Relini, Fabrizio Chiti
A distinctive characteristic of amyloid fibrils is the β-sheet content that can be typically detected by means of a number of techniques, such as far-UV CD, FTIR, and X-ray fiber diffraction [37,38]. The far-UV CD spectrum of Ct TDP-43 aggregates, prepared as described above, shows a negative peak at ca. 198 nm (Figure 5(A)), which is indicative of aggregates having a random coil content. Although more noisy, a similar far-UV CD spectrum was obtained for FL TDP-43 aggregates, with a negative peak at ca. 194 nm (Figure 5(B)). FL TDP-43 aggregates treated with PK showed a flat CD spectrum without any peak corresponding to a β-sheet secondary structures (data not shown).