Molecular dynamics and experimental investigation of H₂ and O₂ diffusion in [Fe]-hydrogenase

The [Fe]-hydrogenase enzymes are highly efficient H₂ catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. Although these enzymes can occur in several forms, H₂ catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. Significant to the function of hydrogenases is how the surrounding protein structure facilitates substrate-product transfer, and protects the active site H-cluster from inactivation. To elucidate the role of protein structure in O₂ inactivation of [Fe]-hydrogenases, experimental and theoretical investigations have been performed. Molecular dynamics was used to comparatively investigate O₂ and H₂ diffusion in CpI ([Fe]-hydrogenase I from Clostridium pasteurianum). Our preliminary results suggest that H₂ diffuses more easily and freely than O₂, which is restricted to a small number of allowed pathways to and from the active site. These O₂ pathways are located in the conserved active site domain, shown experimentally to have an essential role in active site protection.