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

The [Fe]-hydrogenase enzymes are highly efficient H-2 catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlomydomonas reinhardtii. Although these enzymes can occur in several forms, H-2 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 O-2 inactivation of [Fe]-hydrogenases, experimental and theoretical investigations have been performed. Molecular dynamics was used to comparatively investigate O-2 and H-2 diffusion in Cpl ([Fe]-hydrogenase I from Clostridium pasteurianum). our preliminary results suggest that H-2 diffuses more easily and freely than O-2, which is restricted to a small number of allowed pathways to and from the active site. These O-2 pathways are located in the conserved active site domain, shown experimentally to have an essential role in active site protection.