Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis.

Peroxiredoxins (Prxs) constitute a ubiquitous family of Cys-dependent peroxidases that play essential roles in reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides in almost all organisms. Members of the Prx subfamilies show differential oxidizing substrate specificities that await explanations at a molecular level. Among them, alkyl hydroperoxide reductases E (AhpE) is a novel subfamily comprising Mycobacterium tuberculosis AhpE and AhpE-like proteins expressed in some bacteria and archaea. We previously reported that MtAhpE reacts ∼10(4) times faster with an arachidonic acid derived hydroperoxide than with hydrogen peroxide, and suggested that this surprisingly high reactivity was related to the presence of a hydrophobic groove at the dimer interface evidenced in the crystallography structure of the enzyme. In this contribution we experimentally confirmed the existence of an exposed hydrophobic patch in MtAhpE. We found that fatty acid hydroperoxide reduction by the enzyme showed positive activation entropy that importantly contributed to catalysis. Computational dynamics indicated that interactions of fatty acid-derived hydroperoxides with the enzyme properly accommodated them inside the active site and modifies enzyme's dynamics. The computed reaction free energy profile obtained via QM/MM simulations is consistent with a greater reactivity in comparison with hydrogen peroxide. This study represents new insights on the understanding of the molecular basis that determines oxidizing substrate selectivity in the peroxiredoxin family, which has not been investigated at an atomic level so far.

Carbonaceous fraction in PM2.5 of six Latin American cities: Seasonal variations, sources and secondary organic carbon contribution.

Latin American (LatAm) cities are grappling with elevated levels of gaseous and particulate pollutants, which are having detrimental effects on both the local ecosystem and human health. Of particular concern are aerosols with smaller diameters (lower or equal to 2.5 µm, PM2.5), known for their ability to penetrate deep into the respiratory system. While measurements in the region are increasing, they remain limited. This study addresses this gap by presenting the results of a comprehensive, year-long PM2.5 monitoring campaign conducted in six LatAm cities: Buenos Aires, São Paulo, Medellín, San José, Quito and Ciudad de México. Despite all six monitoring sites being urban, they exhibited significant variations in PM2.5 levels, as well as in the content and seasonal behavior of elemental carbon (EC) and organic carbon (OC). Estimations of secondary organic carbon (SOC) using the EC-tracer method revealed a notable SOC relevance across all cities: secondary organic aerosols (SOA) accounted in average for between 19 % to 48 % of the total carbonaceous matter. Source attribution, conducted through the Positive Matrix Factorization (PMF) model, highlights substantial contributions from gasoline and diesel traffic emissions (29 % to 49 % of total carbon, TC), regional biomass burning (21 % to 27 %), and SOA (20 % to 38 %) in all cities, with similar chemical signatures. Additionally, industrial emissions were significant in two cities (Medellín and San José), while two others experienced minor impacts from construction machinery at nearby sites (Buenos Aires and Quito). This comparative analysis underscores the importance of considering not only the thermal optical EC/OC fractions as tracers of sources but also the OC/EC ratio of the PMF factors. This dual approach not only adds depth to the research but also suggests varied methodologies for addressing this crucial environmental concern. This study lays the groundwork for future investigations into the factors influencing the content and seasonality of SOA in the region.

Thiol redox biochemistry: insights from computer simulations.

Thiol redox chemical reactions play a key role in a variety of physiological processes, mainly due to the presence of low-molecular-weight thiols and cysteine residues in proteins involved in catalysis and regulation. Specifically, the subtle sensitivity of thiol reactivity to the environment makes the use of simulation techniques extremely valuable for obtaining microscopic insights. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations on (1) the protonation state of cysteine in protein, (2) two-electron oxidation of thiols by hydroperoxides, chloramines, and hypochlorous acid, (3) mechanistic and kinetics aspects of the de novo formation of disulfide bonds and thiol-disulfide exchange, (4) formation of sulfenamides, (5) formation of nitrosothiols and transnitrosation reactions, and (6) one-electron oxidation pathways.