Structures of Streptococcus pyogenes class A sortase in complex with substrate and product mimics provide key details of target recognition
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Near monodisperse mesoporous silica nanoparticles (MSN) represent a promising and rapidly developing type of mesoporous silica materials; however, the vast data on their synthesis remains unorganized and ill-understood. We systematically studied the formation of MSN under basic and neutral conditions using various temperatures, CTAB concentrations, hydrolyzing agents (triethanolamine, ammonia, phosphate buffers), and media with different colloidal stabilization properties (with ethanol as a cosolvent and monovalent salts). In the typical conditions for the preparation of stable MSN colloids, the particle size was controlled by colloidal stabilization by the medium (solvent type, ionic strength, and surfactant concentration) in agreement with the “aggregative growth” mechanism, rather than by solely the hydrolysis and condensation rates conventionally used for data interpretation in the classical nucleation theory. Medium properties (pH, ion types and concentration, polarity) also defined the efficiency of silica-surfactant cooperative self-assembly, which directly affected the porosity, mesopore size and pore wall thickness. Interestingly, this traditional silica-surfactant route showed a limited effect on the particle size, emphasizing the dominating role of colloidal stabilization in the studied reaction conditions. In situ pH measurements showed that every reaction medium has unique pH evolution profiles depending on the buffer capacity, hydrolysis and condensation rates. Reaction systems that fail to maintain the working pH can lead to non-porous products or undesired particle morphology and size distribution. The established particle formation mechanism allowed us to formulate comprehensive guidelines for preparing relatively concentrated colloids of near monodisperse (PDI 5–15%) mesoporous 30–700 nm silica spheres with variable porosity and mesopore size. Here, these findings will be particularly useful in designing new mesoporous silica-containing materials for biomedical applications.
The main difficulty in simulating diffusion processes at a molecular level in cell microdomains is due to the multiple scales involving nano- to micrometers. Few to many particles have to be simulated and simultaneously tracked while there are exploring a large portion of the space for binding small targets, such as buffers or active sites. Bridging the small and large spatial scales is achieved by rare events representing Brownian particles finding small targets and characterized by long-time distribution. These rare events are the bottleneck of numerical simulations. A naive stochastic simulation requires running many Brownian particles together, which is computationally greedy and inefficient. Solving the associated partial differential equations is also difficult due to the time dependent boundary conditions, narrow passages and mixed boundary conditions at small windows. We present here two reduced modeling approaches for a fast computation of diffusing fluxes in microdomains. The first approach is based on a Markov mass-action law equations coupled to a Markov chain. The second is a Gillespie's method based on the narrow escape theory for coarse-graining the geometry of the domain into Poissonian rates. The main application concerns diffusion in cellular biology, where we compute as an example the distribution of arrival times of calcium ions to small hidden targets to trigger vesicular release.
Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this study, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.
Owing to their excellent properties, austenitic stainless steels are extensively used in boilers, furnaces, molten salt tanks, and other applications that are subjected to extreme mechanical loads and high-temperature conditions. Their high corrosion and creep resistance make them suitable for high-temperature operating environments. Additionally, good fatigue resistance and favorable mechanical and visual properties are essential. However, the premature failure of several components at elevated temperatures has been previously reported. Although the failure analysis of components in service is complex, processes such as cold work and welding have been identified as contributing factors to the performance degradation of these steels. This study aims to analyze the various documented failure modes and mechanisms in austenitic steels, including creep, cracking, stress relaxation cracking, and fatigue, to better understand the multi-objective design requirements for these alloys as structural materials for high-temperature molten salt tanks in Concentrating Solar Power (CSP) plants. Stabilized austenitic grades, such as AISI 347H, demonstrate superior resistance to creep and corrosion-related degradation when compared to non-stabilized grades like AISI 316L at temperatures relevant to concentrated solar power (CSP) applications. In contrast, nickel-based alloys offer enhanced corrosion resistance, albeit at a higher cost. This review underscores that creep, stress relaxation cracking, and thermo-mechanical fatigue are the predominant long-term failure risks in CSP hot tanks.
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Recently, an internal gelation study demonstrated that the use of heated urea and hexamethylenetetramine can have a pronounced impact on the porosity and sintering characteristics of cerium dioxide (CeO 2 ) microspheres. This effort has identified process variables that can significantly change the initial porosity of the CeO 2 microspheres with slight modifications. A relatively small difference in the sample preparation of cerium ammonium nitrate and ammonium hydroxide solution had a large reproducible impact on the porosity and slow pour density of the produced microspheres. Increases in the gelation temperature as small as 0.5 K also produced a noticeable increase in the slow pour density. If the gelation temperature was increased too high, the use of the heated hexamethylenetetramine and urea was no longer observed to be effective in increasing the porosity of the CeO 2 microspheres. In conclusion, the final process variable was the amount of dispersing agent, Span™ 80, which can increase the slow pour density and produce significantly smaller microspheres.
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Solvothermal reactions of Cd(II) or Mn(II) ions with 4'-(4-carboxylphenyl)-2,2':6',2{sup -}terpyridine acid (Hcpt) and thiophene-2,5-dicarboxylic acid (H{sub 2}tpd) resulted in the formation of two isostructrual coordination networks ([M{sub 2}(cpt){sub 2}(tpd)]·3.5H{sub 2}O){sub n} (M=Cd, 1; M=Mn, 2). These complexes have been characterized by single-crystal X-ray diffraction analyses, infrared spectra (IR), elemental analyses, and powder X-ray diffraction (PXRD). Complexes 1 and 2, formed by the cpt{sup −} and tpd{sup 2−} bidentate connectors, have a 3D framework with a 3-connected, uninodal 10{sup 3}-ths topology possessing an unusual eight-fold [4*2] interpenetration mode. In addition, the ths cage has a long intracage M⋯M distance. In contrast, only a 1D coordination network ([CdCl(cpt)]·3.75H{sub 2}O){sub n} (3) was obtained under similar conditions while in the absence of the H{sub 2}tpd ligand. Compound 3 is propagated only by the [CdCl(cpt)] unit, which illustrated that the incorporation of the cpt{sup −} and Cl{sup −} ligands to form a 1D network. The distinct ancillary anions (tpd{sup 2−} or Cl{sup −}) play a critical role in determining the coordination features and the network connectivity of metal ions. This work presents a successful route to preparing rare eight-fold [4*2] interpenetrated networks. - Highlights: • A ths-type network with an eight-fold [4*2] interpenetration mode is rare. • Combining elongated ligands facilitate the eight-fold interpenetrated networks. • This ths-type cage features longe intracage M⋯M distances. • The chloride anion cannot help the forming of 3D frameworks. • The integration of bulky and multi-carboxylate ligands helps the forming of ths-type MOFs.
Oil biodegradation as a weathering process has been extensively investigated over the years, especially after the Deepwater Horizon blowout. In this study, we performed microcosm experiments at 5 °C with chemically dispersed oil in non-amended seawater. We link biodegradation processes with microbial community and metagenome dynamics and explain the succession based on substrate specialization. Reconstructed genomes and 16S rRNA gene analysis revealed that Bermanella and Zhongshania were the main contributors to initial n-alkane breakdown, while subsequent abundances of Colwellia and microorganisms closely related to Porticoccaceae were involved in secondary n-alkane breakdown and beta-oxidation. Cycloclasticus, Porticoccaceae and Spongiiabcteraceae were associated with degradation of mono- and poly-cyclic aromatics. Successional pattern of genes coding for hydrocarbon degrading enzymes at metagenome level, and reconstructed genomic content, revealed a high differentiation of bacteria involved in hydrocarbon biodegradation. Finally, a cooperation among oil degrading microorganisms is thus needed for the complete substrate transformation.