Pathways of H2 toward the active site of [NiFe]-hydrogenase

Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H-2), but little is known about the diffusion of H-2 toward the active site. Here we analyze pathways for H-2 permeation using molecular dynamics (MD) simulations in explicit solvent. Various MD simulation replicates were done, to improve the sampling of the system states. H-2 easily permeates hydrogenase in every simulation and it moves preferentially in channels. All H-2 molecules that reach the active site made their approach from the side of the Ni ion. H-2 is able to reach distances of < 4 angstrom from the active site, although after 6 A permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H-2 inside the protein and at lower distances from the active site. This valine can be a control point in the H-2 access to the active center.