Hard x-ray spectroscopy in NaxCoO2 and superconducting NaxCoO2 - yH2O: A view on the bulk Co electronic properties

The electronic properties of Co in bulk Na0.7CoO2 and the superconducting hydrated compound Na0.35CoO2 - y H2O have been investigated by x-ray absorption spectroscopy (XAS) and resonant inelastic x-ray scattering (RIXS) using hard x-rays. The XAS spectra at the Co K-edge were measured in both compounds with two different polarization directions. The changes in the XAS spectra upon hydration and their polarization dependence are well accounted for by linear muffin- tin orbital calculations in the local density approximation. The underlying electronic structure indicates the strong hybridization between the Co 3d and O 2p states in both compounds, while the electron localization is enhanced in the hydrated compound due to the increase of the Co-Co interplanar distance. The Co K pre-edge further highlights the splitting of the d band as a result of the crystal field effect and demonstrates the Co valency increase when Na0.7CoO2 is hydrated. The RIXS spectra measured at the Co K-edge show an energy loss feature around 10 eV in both compounds in fair agreement with the calculated dynamical structure factor. The RIXS feature is associated to a damped plasmon excitation.Comment: 8 page

Application of third generation synchrotron source to studies of noncrystalline materials : In-Se amorphous films

The local structure of vacuum evaporated In-Se amorphous films, containing 50, 60, and 66 at .% Se, was studied using differential anomalous X -ray scattering and extended X -ray absorption fine structure. Both intensity and absorption spectra were measured in the vicinity of the absorption K -edge of Se. The differential anomalous X -ray scattering data were converted to real space by the inverse Fourier transform yielding the differential radial distribution functions. The obtained results provide evidence for the presence of Se-In spatial correlations for In5 0 Se50 and Se-In and Se-Se correlations for In40 Se60 and In34 Se66 within the first coordination sphere

Zn-induced interactions between SARS-CoV-2 orf7a and BST2/Tetherin

We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity. Our explanation for this behavior is that, when BST2 gets in contact with Zn bound to the orf7a Cys(15) ligand, it has the ability of displacing the metal owing to the creation of a new disulfide bridge across the two proteins. The formation of this BST2-orf7a complex destabilizes BST2 dimerization, thus impairing the antiviral activity of the latter

Nuclear target search at the single molecule level: protein interactions define the exploration landscape

Gene regulation relies on highly mobile transcription factors (TFs) exploring the nucleoplasm in search of their targets. Our view of the nucleus has evolved from that of an isotropic and homogenous reactor to that of a highly organized yet very dynamic organelle. However important questions remain on how these regulatory factors explore the nuclear environment in search of their DNA or protein targets, and how their exploration strategy affects the kinetics of transcriptional regulation. We implemented a single-molecule tracking assay to determine the TFs dynamics using photoactivatable tags in human cells. We investigated the mobility of several nuclear proteins, including the transcription factor c-Myc and the elongation factor P-TEFb. We found that, while their diffusion speed was comparable, these proteins largely differed in terms of their exploration geometry. We discovered that c-Myc is a global explorer diffusing in the nucleus without spatial constraints. In contrast, the positive transcription elongation factor P-TEFb is a local explorer that oversamples its environment, constrained by a fractal nuclear architecture. Consequently, each c-Myc molecule is equally available for all nuclear sites while P-TEFb reaches its targets in a position-dependent manner. We also measured the mobility of a P-TEFb mutant in which the interaction with the CTD of the RNA Pol II was truncated. In this case, the single-molecule experiments suggested a global exploration of the P-TEFb mutant, consistent with free diffusion. Our observations are in line with a model in which the exploration geometry of TFs is constrained by their interactions and not by exclusion properties. Our findings have strong implications on how proteins react in the nucleus and how their function can be regulated in space and time

The role of Zn ions in the interaction between SARS-CoV-2 orf7a protein and BST2/tetherin

In this paper, we provide evidence that Zn2+ ions play a role in the SARS-CoV-2 virus strategy to escape the immune response mediated by the BST2-tetherin host protein. This conclusion is based on sequence analysis and molecular dynamics simulations as well as X-ray absorption experiments [1]

The role of Zn ions in the interaction between SARS-CoV-2 orf7a protein and BST2/tetherin

In this paper, we provide evidence that Zn2+ ions play a role in the SARS-CoV-2 virus strategy to escape the immune response mediated by the BST2-tetherin host protein. This conclusion is based on sequence analysis and molecular dynamics simulations as well as X-ray absorption experiments

Metal ion binding in wild-type and mutated frataxin: a stability study

This work studies the stability of wild-type frataxin and some of its variants found in cancer tissues upon Co2+ binding. Although the physiologically involved metal ion in the frataxin enzymatic activity is Fe2+, as it is customarily done, Co2+ is most often used in experiments because Fe2+ is extremely unstable owing to the fast oxidation reaction Fe2+ → Fe3+. Protein stability is monitored following the conformational changes induced by Co2+ binding as measured by circular dichroism, fluorescence spectroscopy, and melting temperature measurements. The stability ranking among the wild-type frataxin and its variants obtained in this way is confirmed by a detailed comparative analysis of the XAS spectra of the metal-protein complex at the Co K-edge. In particular, a fit to the EXAFS region of the spectrum allows positively identifying the frataxin acidic ridge as the most likely location of the metal-binding sites. Furthermore, we can explain the surprising feature emerging from a detailed analysis of the XANES region of the spectrum, showing that the longer 81-210 frataxin fragment has a smaller propensity for Co2+ binding than the shorter 90-210 one. This fact is explained by the peculiar role of the N-terminal disordered tail in modulating the protein ability to interact with the metal

Oxide phase characterization in simulated high burn-up UO2 fuels in the early stages of a nuclear severe accident

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