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Diagram, valence-to-core, and hypersatellite Kβ X-ray transitions in metallic chromium
Publication . Zeeshan, Faisal; Hoszowska, Joanna; Dousse, Jean Claude; Sokaras, Dimosthenis; Weng, Tsu Chien; Alonso-Mori, Roberto; Kavčič, Matjaz; Guerra, Mauro; Sampaio, Jorge Miguel; Parente, Fernando; Indelicato, Paul; Marques, José Pires; Santos, José Paulo; LIBPhys-UNL; DF – Departamento de Física; John Wiley & Sons, Ltd.
We report on measurements of the Kβ diagram, valence-to-core (VtC), and hypersatellite X-ray spectra induced in metallic Cr by photon single and double K-shell ionization. The experiment was carried out at the Stanford Synchrotron Radiation Lightsource using the seven-crystal Johann-type hard X-ray spectrometer of the beamline 6-2. For the Kβ diagram and VtC transitions, the present study confirms the line shape features observed in previous works, whereas the K h β hypersatellite transition was found to exhibit a complex spectral line shape and a characteristic low-energy shoulder. The energy shift of the hypersatellite relative to the parent diagram line was deduced from the measurements and compared with the result of extensive multiconfiguration Dirac–Fock (MCDF) calculations. A very good agreement between experiment and theory was found. The MCDF calculations were also used to compute the theoretical line shape of the hypersatellite. A satisfactory agreement was obtained between the overall shapes of the experimental and theoretical spectra, but deviations were observed on the low- and high-energy flanks of the hypersatellite line. The discrepancies were explained by chemical effects, which were not considered in the MCDF calculations performed for isolated atoms.
Theoretical and experimental determination of K - And L -shell x-ray relaxation parameters in Ni
Publication . Guerra, Mauro; Sampaio, J. M.; Parente, F.; Indelicato, P.; Hönicke, P.; Müller, M.; Beckhoff, B.; Marques, J. P.; Santos, J. P.; LIBPhys-UNL; DF – Departamento de Física; American Physical Society
Fluorescence yields (FY) for the Ni K and L shells were determined by a theoretical and an experimental group within the framework of the International Initiative on X-ray Fundamental Parameters (FPs) collaboration. Coster-Kronig (CK) parameters were also measured for the L shell of Ni. Theoretical calculations of the same parameters were performed using the Dirac-Fock method, including relativistic and QED corrections. The experimental values for the FY and CK were determined at the PTB laboratory in the synchrotron radiation facility BESSY II, Berlin, Germany, and are compared to the corresponding calculated values.
Precise x-ray energies of gadolinium determined by a combined experimental and theoretical approach
Publication . Ménesguen, Y.; Lépy, M. C.; Ito, Y.; Yamashita, M.; Fukushima, S.; Polasik, M.; Słabkowska, K.; Syrocki; Wȩder, E.; Indelicato, P.; Marques, J. P.; Sampaio, J. M.; Guerra, M.; Parente, F.; Santos, J. P.; LIBPhys-UNL; DF – Departamento de Física; PERGAMON-ELSEVIER SCIENCE LTD
We combined different experimental techniques with a theoretical approach to determine a consistent set of diagram lines energies and binding energies. We propose an original approach consisting in determining the mass attenuation coefficients in an energy range covering the L-, M- and N- absorption edges, including a detailed evaluation of the associated uncertainties, to derive precisely the binding energies. We investigated the Lα, Lβ and M spectra of Gd with an independantly calibrated high-resolution anti-parallel double-crystal x-ray spectrometer. All the lines were identified and found in excellent agreement with the binding energies previously derived. Morever, we identified for the first time M5−O2, M4−O2,3 and M4−N2,3 diagram lines.
Resistance of mRNAs with AUG-proximal nonsense mutations to nonsense-mediated decay reflects variables of mRNA structure and translational activity
Publication . Pereira, Francisco J C; Teixeira, Alexandre R. S.; Kong, Jian; Barbosa, Cristina; Silva, Ana Luísa; Marques-Ramos, Ana; Liebhaber, Stephen A.; Romão, Luísa; NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM); Centro de Investigação em Genética Molecular Humana (CIGMH); Oxford University Press
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that recognizes and selectively degrades mRNAs carrying premature termination codons (PTCs). The level of sensitivity of a PTC-containing mRNA to NMD is multifactorial. We have previously shown that human β-globin mRNAs carrying PTCs in close proximity to the translation initiation AUG codon escape NMD. This was called the 'AUG-proximity effect'. The present analysis of nonsense codons in the human α-globin mRNA illustrates that the determinants of the AUG-proximity effect are in fact quite complex, reflecting the ability of the ribosome to re-initiate translation 3′ to the PTC and the specific sequence and secondary structure of the translated ORF. These data support a model in which the time taken to translate the short ORF, impacted by distance, sequence, and structure, not only modulates translation re-initiation, but also impacts on the exact boundary of AUG-proximity protection from NMD.
Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus
Publication . Sena, Filipa V.; Sousa, Filipe M.; Oliveira, Ana Sofia F.; Soares, Cláudio M.; Catarino, Teresa; Pereira, Manuela M.; Molecular, Structural and Cellular Microbiology (MOSTMICRO); Instituto de Tecnologia Química e Biológica António Xavier (ITQB); DQ - Departamento de Química; Elsevier
Type-II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains and the only enzymes with NADH:quinone oxidoreductase activity expressed in Staphylococcus aureus (S. aureus), one of the most common causes of clinical infections. NDH-2s are members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, having a flavin adenine dinucleotide, FAD, as prosthetic group and NAD(P)H as substrate. The establishment of a Charge-Transfer Complex (CTC) between the isoalloxazine ring of the reduced flavin and the nicotinamide ring of NAD+ in NDH-2 was described, and in this work we explored its role in the kinetic mechanism using different electron donors and electron acceptors. We observed that CTC slows down the rate of the second half reaction (quinone reduction) and determines the effect of HQNO, an inhibitor. Also, protonation equilibrium simulations clearly indicate that the protonation probability of an important residue for proton transfer to the active site (D302) is influenced by the presence of the CTC. We propose that CTC is critical for the overall mechanism of NDH-2 and possibly relevant to keep a low quinol/quinone ratio and avoid excessive ROS production in vivo.
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Fundação para a Ciência e a Tecnologia
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5876
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UID/Multi/04046/2013