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  • 1
    Publication Date: 2015-09-30
    Description: Certain proteins utilize the high reactivity of radicals for catalysing chemically challenging reactions. These proteins contain or form a radical and therefore named ‘radical enzymes’. Radicals are introduced by enzymes themselves or by (re)activating proteins called (re)activases. The X-ray structures of radical enzymes and their (re)activases revealed some structural features of these molecular apparatuses which solved common enigmas of radical enzymes—i.e. how the enzymes form or introduce radicals at the active sites, how they use the high reactivity of radicals for catalysis, how they suppress undesired side reactions of highly reactive radicals and how they are (re)activated when inactivated by extinction of radicals. This review highlights molecular architectures of radical B 12 enzymes, radical SAM enzymes, tyrosyl radical enzymes, glycyl radical enzymes and their (re)activating proteins that support their functions. For generalization, comparisons of the recently reported structures of radical enzymes with those of canonical radical enzymes are summarized here.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 2
    Publication Date: 2014-11-28
    Description: Invasive aspergillosis is an important cause of morbidity and mortality in immunocompromised patients. Diagnosis of this infection frequently employs detection of the circulating galactomannan in the patient serum using enzyme immunoassay (EIA), a highly sensitive and specific system. Although there are many structural studies of the galactomannan of Aspergillus fumigatus , some inconsistencies are present in these results. In this study, to clarify the relationship between the growth conditions and structure of the galactomannans, we cultured A. fumigatus using two distinct yeast/fungal cultivation media, i.e. the yeast extract–peptone–dextrose (YPD) medium and yeast nitrogen base (YNB) medium. Galactomannans prepared from the resulting culture supernatants were structurally characterized by 1 H and 13 C nuclear magnetic resonance, methylation analysis, acetolysis and α-mannosidase degradation. These assays revealed that the galactomannan from the YPD cultivation had short β-1,5-linked galactofuranose (Gal f ) oligosaccharide chains in both the O- and N-linked carbohydrate moieties, while the galactomannan from the YNB cultivation incorporated long Gal f oligosaccharide chains. The galactomannans derived from the two culture conditions significantly differed in reactivity based on the EIA diagnostic system. We also demonstrated the presence of a novel Gal f -containing branched oligosaccharide in the O-linked moiety.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 3
    Publication Date: 2015-05-22
    Description: Si–Si atomic columns separated by 45 pm were successfully resolved with a 300-kV aberration-corrected scanning transmission electron microscope (STEM) equipped with a cold-field emission gun. Using a sufficiently small Gaussian effective source size and a 0.4-eV energy spread at 300 kV, the focused electron probe on the specimen was simulated to be sub-50 pm. Image simulation showed that the present probe condition was sufficient to resolve 45 pm Si–Si dumbbells. A silicon crystalline specimen was observed from the [114] direction with a high-angle annular dark field STEM and the intensity profile showed 45 pm separation. A spot corresponding to (45 pm) –1 was confirmed in the power spectrum of the Fourier transform.
    Print ISSN: 0022-0744
    Electronic ISSN: 1477-9986
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2016-02-14
    Description: Skyrmions are topologically protected nanoscale magnetic spin entities in helical magnets. They behave like particles and tend to form hexagonal close-packed lattices, like atoms, as their stable structure. Domain boundaries in skyrmion lattices are considered to be important as they affect the dynamic properties of magnetic skyrmions. However, little is known about the fine structure of such skyrmion domain boundaries. We use differential phase contrast scanning transmission electron microscopy to directly visualize skyrmion domain boundaries in FeGe 1– x Si x induced by the influence of an "edge" of a crystal grain. Similar to hexagonal close-packed atomic lattices, we find the formation of skyrmion "7" domain boundary, whose orientation relationship is predicted by the coincidence site lattice theory to be geometrically stable. On the contrary, the skyrmion domain boundary core structure shows a very different structure relaxation mode. Individual skyrmions can flexibly change their size and shape to accommodate local coordination changes and free volumes formed at the domain boundary cores. Although atomic rearrangement is a common structural relaxation mode in crystalline grain boundaries, skyrmions show very unique and thus different responses to such local lattice disorders.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 5
    Publication Date: 2016-11-13
    Description: In deformation processes, the presence of grain boundaries has a crucial influence on dislocation behavior; these boundaries drastically change the mechanical properties of polycrystalline materials. It has been considered that grain boundaries act as effective barriers for dislocation glide, but the origin of this barrier-like behavior has been a matter of conjecture for many years. We directly observe how the motion of individual dislocations is impeded at well-defined high-angle and low-angle grain boundaries in SrTiO 3 , via in situ nanoindentation experiments inside a transmission electron microscope. Our in situ observations show that both the high-angle and low-angle grain boundaries impede dislocation glide across them and that the impediment of dislocation glide does not simply originate from the geometric effects; it arises as a result of the local structural stabilization effects at grain boundary cores as well, especially for low-angle grain boundaries. The present findings indicate that simultaneous consideration of both the geometric effects and the stabilization effects is necessary to quantitatively understand the dislocation impediment processes at grain boundaries.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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