A Novel OxyR Sensor and Regulator of Hydrogen Peroxide Stress with One Cysteine Residue in Deinococcus radiodurans

In bacteria, OxyR is a peroxide sensor and transcription regulator, which can sense the presence of reactive oxygen species and induce antioxidant system. When the cells are exposed to H2O2, OxyR protein is activated via the formation of a disulfide bond between the two conserved cysteine residues (C199 and C208). In Deinococcus radiodurans, a previously unreported special characteristic of DrOxyR (DR0615) is found with only one conserved cysteine. dr0615 gene mutant is hypersensitive to H2O2, but only a little to ionizing radiation. Site-directed mutagenesis and subsequent in vivo functional analyses revealed that the conserved cysteine (C210) is necessary for sensing H2O2, but its mutation did not alter the binding characteristics of OxyR on DNA. Under oxidant stress, DrOxyR is oxidized to sulfenic acid form, which can be reduced by reducing reagents. In addition, quantitative real-time PCR and global transcription profile results showed that OxyR is not only a transcriptional activator (e.g., katE, drb0125), but also a transcriptional repressor (e.g., dps, mntH). Because OxyR regulates Mn and Fe ion transporter genes, Mn/Fe ion ratio is changed in dr0615 mutant, suggesting that the genes involved in Mn/Fe ion homeostasis, and the genes involved in antioxidant mechanism are highly cooperative under extremely oxidant stress. In conclusion, these findings expand the OxyR family, which could be divided into two classes: typical 2-Cys OxyR and 1-Cys OxyR

Introducing a standard method for experimental determination of the solvent response in laser pump, x-ray probe time-resolved wide-angle x-ray scattering experiments on systems in solution

WOS:000323520600021International audienceIn time-resolved laser pump, X-ray probe wide-angle X-ray scattering experiments on systems in solution the structural response of the system is accompanied by a solvent response. The solvent response is caused by reorganization of the bulk solvent following the laser pump event, and in order to extract the structural information of the solute, the solvent response has to be treated. Methodologies capable of doing so include both theoretical modelling and experimental determination of the solvent response. In the work presented here, we have investigated how to obtain a reproducible solvent response-the solvent term-experimentally when applying laser pump, X-ray probe time-resolved wide-angle X-ray scattering. The solvent term describes difference scattering arising from the structural response of the solvent to changes in the hydrodynamic parameters: pressure, temperature and density. We present results based on NIR and dye mediated solvent heating, and demonstrate that the solvent response is independent of the heating method. The NIR heating is shown to be rendered unusable by higher order effects under certain experimental conditions, while the dye mediated solvent heating is demonstrated to exhibit first order behaviour with respect to the amount of energy deposited in the solution. We introduce a standardized method for recording solvent responses in laser pump, X-ray probe time-resolved X-ray wide-angle scattering experiments by using dye mediated solvent heating. Furthermore, we have generated a library of solvent terms, which can be used to describe the solvent term in any TRWAXS experiment, and made it available online

Dynamical Properties of a Ru/MgAl_(2)O_4 Catalyst during Reduction and Dry Methane Reforming

Combined in situ small- and wide-angle X-ray scattering (SAXS/WAXS) studies were performed in a new laboratory setup to investigate the dynamical properties of a ruthenium/spinel ( Ru/MgAl_2O_4) catalyst, w(Ru) = 4 wt %, during the reduction and subsequent dry methane reforming. The Ru particles in the fresh catalyst sample were found to be partially oxidized. High-resolution transmission electron microscopy (HRTEM) indicated a coexistence of pure Ru and RuO_2 nanoparticles. Reduction in hydrogen occurred at a temperature between 373 and 393 K. The mean particle diameter as refined from SAXS of the size regime attributed to scattering from Ru/RuO_2-particles decreases slightly by about 0.2 nm during the reduction. Dry methane reforming experiments were performed in a temperature interval from 723 to 1023 K by applying a gas mixture of carbon dioxide and methane in molar ratio of 3:1. The catalyst did not show any deactivation during the experiment of overall 32 h, indicated by stable turnover frequencies for methane. The mean Ru-particle diameter remained constant during the dry methane reforming experiments, revealing a high sintering stability of the Ru/MgAl_2O_4 catalyst

Computational design of ligand binding is not a solved problem

Computational design has been very successful in recent years: multiple novel ligand binding proteins as well as enzymes have been reported. We wanted to know in molecular detail how precise the predictions of the interactions of protein and ligands are. Therefore, we performed a structural analysis of a number of published receptors designed onto the periplasmic binding protein scaffold that were reported to bind to the new ligands with nano- to micromolar affinities. It turned out that most of these designed proteins are not suitable for structural studies due to instability and aggregation. However, we were able to solve the crystal structure of an arabinose binding protein designed to bind serotonin to 2.2 Å resolution. While crystallized in the presence of an excess of serotonin, the protein is in an open conformation with no serotonin bound, although the side-chain conformations in the empty binding pocket are very similar to the conformations predicted. During subsequent characterization using isothermal titration calorimetry, CD, and NMR spectroscopy, no indication of binding could be detected for any of the tested designed receptors, whereas wild-type proteins bound their ligands as expected. We conclude that although the computational prediction of side-chain conformations appears to be working, it does not necessarily confer binding as expected. Hence, the computational design of ligand binding is not a solved problem and needs to be revisited