Correction to "On Atomistic Models for Molecular Oxygen"

Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen

Molecular oxygen (O2) is essential for life, and continuous effort has been made to understand its pathways in cellular respiration with all-atom (AA) molecular dynamics (MD) simulations of, e.g., membrane permeation or binding to proteins. To reach larger length scales with models, such as curved membranes in mitochondria or caveolae, coarse-grained (CG) simulations could be used at much lower computational cost than AA simulations. Yet a CG model for O2 is lacking. In this work, a CG model for O2 is therefore carefully selected from the Martini 3 force field based on criteria including size, zero charge, nonpolarity, solubility in nonpolar organic solvents, and partitioning in a phospholipid membrane. This chosen CG model for O2 (TC3 bead) is then further evaluated through the calculation of its diffusion constant in water and hexadecane, its permeability rate across pure phospholipid- and cholesterol-containing membranes, and its binding to the T4 lysozyme L99A protein. Our CG model shows semiquantitative agreement between CG diffusivity and permeation rates with the corresponding AA values and available experimental data. Additionally, it captures the binding to hydrophobic cavities of the protein, aligning well with the AA simulation of the same system. Thus, the results show that our O2 model approximates the behavior observed in the AA simulations. The CG O2 model is compatible with the widely used multifunctional Martini 3 force field for biological simulations, which will allow for the simulation of large biomolecular systems involved in O2's transport in the body.

Structural basis for bacterial energy extraction from atmospheric hydrogen

Diverse aerobic bacteria use atmospheric H₂ as an energy source for growth and survival¹. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments^2,3. Atmospheric H₂ oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily^4,5. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H₂ amid ambient levels of the catalytic poison O₂ and how the derived electrons are transferred to the respiratory chain¹. Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H₂ to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H₂ at the expense of O₂, and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H₂ oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H₂ oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H₂ in ambient air.

Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations

NOX5 is a member of the NADPH oxidase family which is dedicated to the production of reactive oxygen species. The molecular mechanisms governing transmembrane electron transfer (ET) that permits to shuttle electrons over the biological membrane have remained elusive for a long time. Using computer simulations, we report conformational dynamics of NOX5 embedded within a realistic membrane environment. We assess the stability of the protein within the membrane and monitor the existence of cavities that could accommodate dioxygen molecules. We investigate the heme-to-heme electron transfer. We find a reaction free energy of a few tenths of eV (ca. −0.3 eV) and a reorganization free energy of around 1.1 eV (0.8 eV after including electrostatic induction corrections). The former indicates thermodynamically favorable ET, while the latter falls in the expected values for transmembrane inter-heme ET. We estimate the electronic coupling to fall in the range of the μeV. We identify electron tunneling pathways showing that not only the W378 residue is playing a central role, but also F348. Finally, we reveal the existence of two connected O₂₋binding pockets near the outer heme with fast exchange between the two sites on the nanosecond timescale. We show that when the terminal heme is reduced, O₂ binds closer to it, affording a more efficient tunneling pathway than when the terminal heme is oxidized, thereby providing an efficient mechanism to catalyze superoxide production in the final step. Overall, our study reveals some key molecular mechanisms permitting reactive oxygen species production by NOX5 and paves the road for further investigation of ET processes in the wide family of NADPH oxidases by computer simulations.