Computational Study of Gas Diffusion Pathways in [FeFe]-Hydrogenase

Abstract

The photobiological generation of hydrogen gas (H2) by green alga is a promising method for affordable H2 production. One of the key enzymes involves in this process is the [FeFe]-hydrogenase, which catalyzes the H2 generation reaction at its catalytic center - H-cluster. There are two major gas diffusion pathways in [Fefe]-hydrogenase to allow the produced H2 to leave the enzyme. However, small gas molecule such as O2 or CO can also transport along those pathways and inactivate the enzyme rapidly by reaction with the H-cluster. In this research, we used molecular dynamics method to study the gas diffusion pathways in [FeFe]-hydrogenase. The hydrogenases investigated are DdH from Desulfovibrio desulfuricans and CpI from Clostridium pasteurianum. Two methodologies, implicit ligand sampling and adaptive biasing force, were applied to investigate the free energy profiles along the pathways for O2 and CO. Out results indicate that the gas diffusion pathways in DdH are more favorable for gas transport than the ones in CpI. We also found several free energy barriers along the pathways, preventing the gas molecule to further transport to the H-cluster. However, the rate limiting step for the inactivation process may not be the gas diffusion, but the reaction that the gas molecule binds to the H-cluster. Nevertheless, raising the free energy barriers along the pathways is still helpful to slow down the inactivation rate and allow the enzyme less sensitive to O2.