Function Of Redox Conditions Research Articles

Structural basis of a redox-dependent conformational switch that regulates the stress kinase p38α

Many functional aspects of the protein kinase p38α have been illustrated by more than three hundred structures determined in the presence of reducing agents. These structures correspond to free forms and complexes with activators, substrates, and inhibitors. Here we report the conformation of an oxidized state with an intramolecular disulfide bond between Cys119 and Cys162 that is conserved in vertebrates. The structure of the oxidized state does not affect the conformation of the catalytic site, but alters the docking groove by partially unwinding and displacing the short αD helix due to the movement of Cys119 towards Cys162. The transition between oxidized and reduced conformations provides a mechanism for fine-tuning p38α activity as a function of redox conditions, beyond its activation loop phosphorylation. Moreover, the conformational equilibrium between these redox forms reveals an unexplored cleft for p38α inhibitor design that we describe in detail.

300-fold higher neuro- and immunotoxicity from low-redox transformation of carbamazepine

Current challenges in (eco)toxicology are in understanding the transformation of (reactive) substances, and how transformation affects toxic modes of action. Empirical assessment of transformation products of, practically an infinite number of substances, via experimentation, is impossible. Predicting transformation products for (benchmarking) compounds from conditions, facilitates risk analyses. This study applied calculus to predict transformation products of an important environmental and medicinal/toxicological marker, carbamazepine. As radicals are ubiquitous in humans and the environment, we looked into radical-mediated transformations of carbamazepine as a benchmark. We calculated proportions of their speciation states as function of redox conditions, which we took as pH and O2 concentration, describing transformation via covalent and ionic interactions. Formation of ring-contracted products with neuro-immunological activity is thermodynamically favored under anaerobic conditions and at low pH. Experimentally observed product distributions and toxicities reflect that pattern. Our predictive method may support toxicity predictions for other substances and conditions 'similar' to the current case study via interpolation. This paves the way for a more coherent, effective and easier risk assessment of transformation products.

Turbidite deposition and diagenesis in the southwestern Black Sea: Implications for biogeochemical cycling in an anoxic basin

The biogeochemical cycles of iron, phosphorus and sulfur are intimately linked and the fate of these elements is highly redox-dependent. Under anoxic conditions, iron is reduced to Fe(II), for an important part driven by reaction with sulfide. Reduction and sulfidation diminish the affinity of iron for phosphorus, thereby affecting sedimentary phosphorus retention. The coupled cycling of iron-phosphorus-sulfur as a function of redox conditions thereby helps control nutrient availability and primary productivity in marine systems. The Black Sea is the world's largest permanently stratified basin with a strong gradient from oxic surface waters to anoxic and strongly sulfidic deep waters, and is therefore well-suited to investigate redox-dependent changes in coupled iron-phosphorus-sulfur cycling. The presence of sulfide in the deep Black Sea alters the chemical speciation of iron (Fe) and phosphorus (P) in particulate matter in the water column and sediment. These alterations and their impact are poorly constrained for turbidites, which are deposits formed by mass transport from the continental slope into the deep basin of the Black Sea through turbidity currents. Here, we compare the geochemistry of sediments on the southwestern (SW) Black Sea slope overlain by oxygenated waters (234 m below sea surface, mbss) with that of a sediment record with turbidite intervals from the sulfidic SW deep basin (2169 mbss). The aims were to investigate the potential of SW slope sediment as source material for turbidites, and to assess the geochemical impact of reaction with sulfide. The bulk chemistry (Al, CaCO3, Fe) of the SW deep Black Sea turbidite intervals was similar to that of SW Black Sea slope sediments (234 m water depth), suggesting that the latter are source material for deep SW Black Sea turbidites. The source sediment is characterized by strong enrichments in highly reactive Fe(III) and Mn phases, high rates of sulfate reduction and the presence of methane. Similar total Fe contents in the slope and deep turbidite sediments suggest that Fe is efficiently retained in the sediment. In contrast, Mn is depleted during down-slope transport and P contents in the turbidite intervals are about 50% lower than in the slope sediment, indicating significant P release during and after turbidite deposition. Calculations using the obtained data and conservative estimates of the areal extent of turbidite deposition in the SW Black Sea indicate that turbidity currents have the potential to impact coupled Fe-P-S biogeochemical cycling by boosting Fe input, dissolved P accumulation, sulfide oxidation and FeS2 burial in the deep Black Sea.

Phosphorus cycling in marine sediments: Advances and challenges

Phosphorus (P) is a critical macronutrient for all living cells, as it provides the phosphate-ester backbone of nucleic acids, plays a crucial role in the transmission of chemical energy by the ATP molecule and is also a structural constituent in many cell components. While P cycling in the marine water column has been the subject of many studies and reviews, many aspects of the sedimentary P cycling remain poorly understood. This is mainly due to low P concentrations in sediments and analytical difficulties associated with isolating distinct P forms from sediment samples. The aim of this review is to highlight the advances made in our understanding of P cycling in marine sediments as a result of improved instrumentation and novel approaches. Some of these techniques range from sediment sequential extractions (SEDEX) to spectroscopic techniques (31P NMR) and innovative isotope tracer experiments (stable oxygen ratios in phosphate, radioactive P isotopes). While our understanding of P cycling has considerably improved, numerous aspects of sedimentary P cycling including the fate of organic P in sediments as a function of redox conditions, organic matter content and burial depth, as well as turnover rates of different sedimentary P compounds remain poorly constrained. The techniques presented in this review, along with yet to be utilized innovative approaches used in soil and lacustrine sediment P research, will play an important role in addressing these important questions and in furthering our understanding of this critical component of the P global biogeochemical cycle.

Oxygen nonstoichiometry, defect equilibria, and thermodynamic characterization of LaMnO3 perovskites with Ca/Sr A-site and Al B-site doping

This work encompasses the thermodynamic characterization of four doped lanthanum manganites, namely La0.6A0.4Mn1−yAlyO3 (A = Ca, Sr and y = 0, 0.4), all showed to be promising redox materials for the solar thermochemical splitting of H2O and CO2 to H2 and CO. We present oxygen nonstoichiometry measurements in the temperature range T = 1573 K–1773 K and oxygen partial pressure range pO2 = 4.5066 × 10−2 bar–9.9 × 10−5 bar. For a given T and pO2, oxygen nonstoichiometry is found to be higher when replacing the divalent dopant Sr in La0.6Sr0.4MnO3 by the divalent Ca but also increases significantly when additionally doping 40 mol-% Al to the Mn-site. La0.6Ca0.4Mn0.6Al0.4O3 revealed the highest mass specific oxygen release, 0.290 mol O2 per kg metal oxide at T = 1773 K and pO2 = 2.360 × 10−3 bar and 0.039 mol kg−1 at T = 1573 K and pO2 = 4.5066 × 10−2 bar. It is shown that the chemical defect equilibrium of all four perovskites can be accurately described by the two simultaneous redox couples Mn4+/Mn3+ and Mn3+/Mn2+. Thermodynamic properties, namely partial molar enthalpy, entropy and Gibbs free energy are consequently extracted from the defect models. Partial molar enthalpy decreases with increasing oxygen nonstoichiometry for the Al-doped perovskites whereas the opposite trend is observed for the others. The enthalpy falls within the range 260–300 kJ mol−1 for all the materials. Equilibrium hydrogen yields upon oxidation with H2O are determined as a function of redox conditions. Although reduction extents of the perovskites are greater compared to CeO2, oxidation with H2O and CO2 is thermodynamically less favorable. This leads to lower mass specific fuel productivity compared to CeO2 under most conditions relevant for solar thermochemical cycles.

Carbon speciation in silicate-C-O-H melt and fluid as a function of redox conditions: An experimental study, in situ to 1.7 GPa and 900 C

Carbon speciation in and partitioning among silicate-saturated C-O-H fluids and (C-O-H)-saturated melts have been determined ~1.7 GPa and 900 °C under reducing and oxidizing conditions. The measurements were conducted in situ while the samples were at the conditions of interest. The solution equilibria were (1) 2CH 4 + Q n = 2CH 3 − + H 2 O + Q n+1 and (2) 2CO 3 2− + H 2 O + 2Q n+1 = HCO 3 − + 2Q n , under reducing and oxidizing conditions, and where the superscript, n , in the Q n -species denotes number of bridging oxygen in the silicate species (Q-species). The abundance ratios, CH 3 /CH 4 and HCO 3 − /CO 3 2− , increase with temperature. The enthalpy change associated with the species transformation differs for fluids and melts and also for oxidized and reduced carbon [Reducing: Δ H (1) fluid = 16 ± 5 kJ/mol, Δ H (1) melt = 50 ± 5 kJ/mol; oxidizing Δ H (2) fluid = 81 ± 14 kJ/mol]. For the exchange equilibrium of CH 4 and CH 3 species between fluid and melt, the temperature-dependent equilibrium constant, (X CH 4 /X CH 3 ) fluid /(X CH 4 /X CH 3 ) melt , yields Δ H = 34 ± 3 kJ/mol. Increased abundance ratios, CH 4 /CH 3 and HCO 3 − /CO 3 2− , lead to increased polymerization of silicate+(C-O-H) melt. Because of such relations, melt transport properties (e.g., viscosity) and element partition coefficients between magmatic liquids, C-O-H fluids, and crystalline phases can vary by more than 100% with speciation changes of C-bearing volatiles upper mantle. These structure effects are more pronounced the higher the pressure and the more mafic the magma.

10.1007/s11495-008-2003-z

The solubility of platinum and palladium in a silicate melt of the composition Di 55 An 35 Ab 10 was determined at 1200°C and 2 kbar pressure in the presence of H2O-H2 fluid at an oxygen fugacity ranging from the HM to WI buffer equilibria. The influence of sulfur on the solubility of platinum in fluid-bearing silicate melt was investigated at a sulfur fugacity controlled by the Pt-PtS equilibrium at 1200°C and a pressure defined in such a way that the $$ f_{H_2 O} $$ and $$ f_{O_2 } $$ values were identical to those of the experiments without sulfur. The experiments were conducted in a high pressure gas vessel with controlled hydrogen content in the fluid. Oxygen fugacity values above the NNO buffer were controlled by solid-phase buffer mixtures using the two-capsule technique. Under more reducing conditions, the contents of H2O and H2 were directly controlled by the argon to hydrogen ratio in a special chamber. The hydrogen fugacity varied from 5.2 × 10−2 bar (HM buffer) to 1230 bar ( $$ X_{H_2 } $$ = 0.5). Pt and Pd contents were measured in quenched glass samples by neutron activation analysis. The results of these investigations showed that the solubility of Pt and Pd increases significantly in the presence of water compared with experiments in dry systems. The content of Pd within the whole range of redox conditions and that of Pt at an oxygen fugacity between the HM to MW buffer reactions are weakly dependent on $$ f_{O_2 } $$ and controlled mainly by water fugacity. This suggests that, in addition to oxide Pt and Pd species soluble at the ppb level in haplobasaltic melts, much more soluble (ppm level) hydroxide complexes of these metals are formed under fluid-excess conditions. Despite a decrease in water fugacity under reducing conditions, Pt solubility increases sharply near the MW buffer. It was shown by electron paramagnetic resonance spectrometry that, in contrast to dry melts, fluid-saturated silicate melts do not contain a pure metal phase (micronuggets). Therefore, the increase in Pt solubility under reducing conditions can be explained by the formation of Pt hydride complexes or Pt-fluid-silicate clusters. At a sulfur fugacity controlled by the Pt-PtS equilibrium, the solubility of Pt in iron-free silicate melts as a function of redox conditions is almost identical to that obtained in the experiments without sulfur at the same water and oxygen fugacity values. These observations also support Pt dissolution in iron-free silicate melts as hydroxide species.

Rare earth element composition of Paleogene vertebrate fossils from Toadstool Geologic Park, Nebraska, USA

Fossil bones and teeth from terrestrial environments encode unique rare earth and trace element (REE and TE) signatures as a function of redox conditions, pH, concentrations of complexing ligands, and water-colloid interactions. This signature is set early in the fossilization process and serves as a paleoenvironmental and paleoclimatic proxy. These signatures can also be used to interpret temporal and spatial averaging within vertebrate accumulations, and can help relocate displaced fossil bones back into stratigraphic context. Rare earth elements in vertebrate fossils from upper Eocene and Oligocene strata of Toadstool Geologic Park, northwestern Nebraska, record mixing and evolution of Paleogene vadose or groundwaters and variations in paleoenvironments. REE signatures indicate that HREE-enriched alkaline groundwater reacted with LREE- and MREE-enriched sediments to produce 3-component mixtures. REE signatures become increasingly LREE- and MREE-enriched toward the top of the studied section as the paleoenvironment became cooler and drier, suggesting that REE signatures may be climate proxies. Time series analysis suggests that REE ratios are influenced by cycles of ca. 1050, 800, 570, 440, and 225 ka, similar to some previously determined Milankovitch astronomical and climate periodicities.

Solubility of platinum and palladium in silicate melts under high water pressure as a function of redox conditions

The solubility of platinum and palladium in a silicate melt of the composition Di55An35Ab10 was determined at 1200°C and 2 kbar pressure in the presence of H2O-H2 fluid at an oxygen fugacity ranging from the HM to WI buffer equilibria. The influence of sulfur on the solubility of platinum in fluid-bearing silicate melt was investigated at a sulfur fugacity controlled by the Pt-PtS equilibrium at 1200°C and a pressure defined in such a way that the \( f_{H_2 O} \) and \( f_{O_2 } \) values were identical to those of the experiments without sulfur. The experiments were conducted in a high pressure gas vessel with controlled hydrogen content in the fluid. Oxygen fugacity values above the NNO buffer were controlled by solid-phase buffer mixtures using the two-capsule technique. Under more reducing conditions, the contents of H2O and H2 were directly controlled by the argon to hydrogen ratio in a special chamber. The hydrogen fugacity varied from 5.2 × 10−2 bar (HM buffer) to 1230 bar (\( X_{H_2 } \) = 0.5). Pt and Pd contents were measured in quenched glass samples by neutron activation analysis. The results of these investigations showed that the solubility of Pt and Pd increases significantly in the presence of water compared with experiments in dry systems. The content of Pd within the whole range of redox conditions and that of Pt at an oxygen fugacity between the HM to MW buffer reactions are weakly dependent on \( f_{O_2 } \) and controlled mainly by water fugacity. This suggests that, in addition to oxide Pt and Pd species soluble at the ppb level in haplobasaltic melts, much more soluble (ppm level) hydroxide complexes of these metals are formed under fluid-excess conditions. Despite a decrease in water fugacity under reducing conditions, Pt solubility increases sharply near the MW buffer. It was shown by electron paramagnetic resonance spectrometry that, in contrast to dry melts, fluid-saturated silicate melts do not contain a pure metal phase (micronuggets). Therefore, the increase in Pt solubility under reducing conditions can be explained by the formation of Pt hydride complexes or Pt-fluid-silicate clusters. At a sulfur fugacity controlled by the Pt-PtS equilibrium, the solubility of Pt in iron-free silicate melts as a function of redox conditions is almost identical to that obtained in the experiments without sulfur at the same water and oxygen fugacity values. These observations also support Pt dissolution in iron-free silicate melts as hydroxide species.

Kinetic Analysis of the Ku-DNA Binding Activity Reveals a Redox-dependent Alteration in Protein Structure That Stimulates Dissociation of the Ku-DNA Complex

Ku is a heterodimeric protein comprising 70- and 80-kDa subunits that participate in the non-homologous end-joining (NHEJ) repair pathway for rejoining DNA double strand breaks. We have analyzed the pre-steady state binding of Ku with various DNA duplex substrates and identified a redox-sensitive Ku-DNA interaction. Pre-steady state analysis of Ku DNA binding was monitored via intrinsic Ku quenching upon binding DNA and revealed that, under fully reduced conditions, binding occurred in a single-step process. Reactions performed under limited reduction revealed a two-step binding process, whereas under fully oxidized conditions, we were unable to detect quenching of Ku fluorescence upon binding DNA. The differential quenching observed under the different redox conditions could not be attributed to two Ku molecules binding to a single substrate or Ku sliding inward on the substrate. Although only modest differences in Ku DNA binding activity were observed in the stoichiometric anisotropy and electrophoretic mobility shift assay studies, as a function of redox conditions, a dramatic difference in the rate of Ku dissociation from DNA was observed. This effect was also induced by diamide treatment of Ku and could be abrogated by dithiothreitol treatment, demonstrating a reversible redox effect on the stability of the Ku-DNA complex. The redox-dependent alteration in Ku-DNA interactions is manifested by a redox-dependent alteration in Ku structure, which was confirmed by limited proteolysis and mass spectrometry analyses. The results support a model for the interaction of Ku with DNA that is regulated by redox status and is achieved by altering the dissociation of the Ku-DNA complex.

Effect of Redox Conditions on the Sorption of Plutonium onto Geological Materials

ABSTRACTThis paper presents the latest results from a programme of generic sorption studies undertaken to increase confidence in data underpinning the performance assessment for a potential high-level radioactive waste repository in Japan. The sorption of plutonium onto basalt and sandstone was studied as a function of redox conditions that ranged from strongly reducing to oxidising. Geochemical modelling was used to aid experimental design and the interpretation of results.