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Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata B

Boubeta, Fernando M., Bari, Sara E., Estrin, Dario A., Boechi, Leonardo
The Journal of physical chemistry 2016 v.120 no.36 pp. 9642-9653
active sites, computer simulation, heme iron, heme proteins, hemoglobin, hydrogen sulfide, ligands
Hydrogen sulfide (H₂S) was recently discovered as a gasotransmitter, capable of coordinating to the heme iron of hemeproteins. H₂S is unique for its ability to render varying concentrations of the nucleophilic conjugate bases (HS– or S²–), either as free or bound species with expected outcomes on its further reactivity. There is no direct evidence about which species (H₂S, HS–, or S²–) coordinates to the iron. We performed computer simulations to address the migration and binding processes of H₂S species to the hemoglobin I of Lucina pectinata, which exhibits the highest affinity for the substrate measured to date. We found that H₂S is the most favorable species in the migration from the bulk to the active site, through an internal pathway of the protein. After the coordination of H₂S, an array of clustered water molecules modifies the active site environment, and assists in the subsequent deprotonation of the ligand, forming Fe(III)–SH–. The feasibility of the second deprotonation of the coordinated ligand is also discussed.