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.