Geometrical fitting of experimental XANES spectra by a full multiple-scattering procedure.

In this paper a new software procedure is presented, named MXAN, able to fit the XANES part (from the edge to about 200 eV) of experimental X-ray absorption data. The method is based on the fitting between the experimental spectrum and several theoretical calculations generated by changing the relevant geometrical parameters of the site around the absorbing atom. The X-ray photo-absorption cross section is calculated using the full multiple-scattering scheme; different choices of the exchange correlation part of the potential can be utilised. To show the potentialities of the method the analysis of the nickel K-edge of the nickel ion in aqueous solution is presented. The procedure is able to recover the correct information on the symmetry and atomic distances from the experimental Ni K-edge XANES spectrum. The recovered structure is found to be independent of the starting conditions, showing the theoretical uniqueness of the structural solution

The MXAN procedure: a new method for analysing the XANES spectra of metalloproteins to obtain structural quantitative information.

The first quantitative analyses are reported of the FeK-edge polarized X-ray absorption near-edge structure (XANES) of a single crystal of the iron protein carbonmonoxy-myoglobin (MbCO) and of its cryogenic photoproduct Mb*CO. The CO—Fe–heme local structure has been determined using a novel fitting procedure, namedMXAN, which is able to fit the XANES part (from the edge to about 200 eV) of experimental X-ray absorption data. This method is based on the comparison between the experimental spectrum and several theoretical spectra that are generated by changing the relevant geometrical parameters of the site around the absorbing atom. The theoretical spectra are derived in the framework of the full multiple-scattering approach. TheMXANprocedure is able to recover information about the symmetry and atomic distances, and the solution is found to be independent of the starting conditions. The extracted local structure of Mb*CO includes an Fe—CO distance of 3.08 (7) Å, with a tilting angle between the heme normal and the Fe—C vector of 37 (7)° and a bending angle between the Fe—C vector and the C—O bond of 31 (5)

MXAN: a new software procedure to perform geometrical fitting of experimental XANES spectra.

A new software procedure, MXAN, to fit experimental XANES spectra is presented here. The method is based on the comparison between the experimental spectrum and several theoretical calculations generated by changing the relevant geometrical parameter of the site around the absorbing atom. The x-ray photoabsorption cross section is calculated using the general multiple-scattering scheme, utilizing a complex Hedin-Lunqvist energy-dependent potential to describe the exchange correlation interaction. Our method has been applied to the study of geometrical environment of the tetrahedral zinc site of the protein superoxide dismutase (SOD). The experimental Zn K-edge XANES spectrum has been fitted in the space of the first shell coordination parameters (ligand distances and angles) following the behavior of the chi-square as a function of the local distortion from the starting crystallographic structure. The recovered structure is found to be independent on the starting conditions, showing the theoretical uniqueness of the structural solution. Strengths and limitations of the application to real systems are also discussed

Iron and copper K-edge XAS study of serotransferrin and ovotransferrin.

The active metal site structure of transferrin with iron and copper atoms is investigated using metal K-XANES. Theoretical analysis of experimental data has been performed on the basis of full multiple-scattering theory. This approach made it possible to study the origin of XANES fine details and to investigate the local structure around active metal sites. A deep insight into the local structure and electronic subsystem of Fe, Cu transferrins is obtained. For example, in the case of Cu substitution of Fe in the active centre, the best fit of theoretical spectra to experiment has been obtained for distances 3% smaller between the Cu atom and the nearest neighbours

Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins

Short Linear Motifs (SLiMs) are functional protein microdomains that typically mediate interactions between a short linear region in one protein and a globular domain in another. Surface Plasmon Resonance assays have been performed to determine the binding affinity between PDZ domain of wild type human PALS1 protein and tetradecapeptides representing the SLiMs sequences of SARS-CoV-1 and SARS-CoV-2 E proteins (E-SLiMs). SARS-CoV-2 E-SLiM binds to the human target protein with a higher affinity compared to SARS-CoV-1, showing a difference significantly greater than previously reported using the F318W mutant of PALS1 protein and shorter target peptides. Moreover, molecular dynamics simulations have provided clear evidence of the structural determinants driving this binding process. Specifically, the Arginine 69 residue in the SARS-CoV-2 E-SLiM is the key residue able to both enhance the specific polar interaction with negatively charged pockets of the PALS1 PDZ domain and reduce significantly the mobility of the viral peptide. These experimental and computational data are reinforced by the comparison of the interaction between the PALS1 PDZ domain with the natural ligand CRB1, as well as the corresponding E-SLiMs of other coronavirus members such as MERS and OCF43. Our results provide a model at the molecular level of the strategies used to mimic the endogenous SLiM peptide in the binding of the tight junctions of the host cell, explaining one of the possible reasons of the severity of the infection and pulmonary inflammation by SARS-CoV-2

Spatial distribution of photoelectrons participating in formation of x-ray absorption spectra

Interpretation of x-ray absorption near-edge structure (XANES) experiments is often done via analyzing the role of particular atoms in the formation of specific peaks in the calculated spectrum. Typically, this is achieved by calculating the spectrum for a series of trial structures where various atoms are moved and/or removed. A more quantitative approach is presented here, based on comparing the probabilities that a XANES photoelectron of a given energy can be found near particular atoms. Such a photoelectron probability density can be consistently defined as a sum over squares of wave functions which describe participating photoelectron diffraction processes, weighted by their normalized cross sections. A fine structure in the energy dependence of these probabilities can be extracted and compared to XANES spectrum. As an illustration of this novel technique, we analyze the photoelectron probability density at the Ti K pre-edge of TiS2 and at the Ti K-edge of rutile TiO2.Comment: Journal abstract available on-line at http://link.aps.org/abstract/PRB/v65/e20511

Probing the active site in single-atom oxygen reduction catalysts via operando X-ray and electrochemical spectroscopy

[[abstract]]Nonnoble metal catalysts are low-cost alternatives to Pt for the oxygen reduction reactions (ORRs), which have been studied for various applications in electrocatalytic systems. Among them, transition metal complexes, characterized by a redox-active single-metal-atom with biomimetic ligands, such as pyrolyzed cobalt–nitrogen–carbon (Co–Nx/C), have attracted considerable attention. Therefore, we reported the ORR mechanism of pyrolyzed Vitamin B12 using operando X-ray absorption spectroscopy coupled with electrochemical impedance spectroscopy, which enables operando monitoring of the oxygen binding site on the metal center. Our results revealed the preferential adsorption of oxygen at the Co2+ center, with end-on coordination forming a Co2+-oxo species. Furthermore, the charge transfer mechanism between the catalyst and reactant enables further Co–O species formation. These experimental findings, corroborated with first-principle calculations, provide insight into metal active-site geometry and structural evolution during ORR, which could be used for developing material design strategies for high-performance electrocatalysts for fuel cell applications.[[notice]]補正完

Preconditioning-induced ischemic tolerance: a window into endogenous gearing for cerebroprotection

Ischemic tolerance defines transient resistance to lethal ischemia gained by a prior sublethal noxious stimulus (i.e., preconditioning). This adaptive response is thought to be an evolutionarily conserved defense mechanism, observed in a wide variety of species. Preconditioning confers ischemic tolerance if not in all, in most organ systems, including the heart, kidney, liver, and small intestine. Since the first landmark experimental demonstration of ischemic tolerance in the gerbil brain in early 1990's, basic scientific knowledge on the mechanisms of cerebral ischemic tolerance increased substantially. Various noxious stimuli can precondition the brain, presumably through a common mechanism, genomic reprogramming. Ischemic tolerance occurs in two temporally distinct windows. Early tolerance can be achieved within minutes, but wanes also rapidly, within hours. Delayed tolerance develops in hours and lasts for days. The main mechanism involved in early tolerance is adaptation of membrane receptors, whereas gene activation with subsequent de novo protein synthesis dominates delayed tolerance. Ischemic preconditioning is associated with robust cerebroprotection in animals. In humans, transient ischemic attacks may be the clinical correlate of preconditioning leading to ischemic tolerance. Mimicking the mechanisms of this unique endogenous protection process is therefore a potential strategy for stroke prevention. Perhaps new remedies for stroke are very close, right in our cells