|Schematic diagram of hydrogen-oxygen reaction taking place in hydrogenase CpI.|
Numerous researchers are exploring the use of enzymes known as hydrogenases as a mechanism for producing molecular hydrogen from microorganisms (i.e., bio-hydrogen). One of the main barriers to this process, however, is that hydrogenase, when exposed to oxygen, eventually shuts down its hydrogen production.
Now researchers at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign have developed a computer simulation that lets them see how and where hydrogen and oxygen travel to reach and exit the hydrogenase’s catalyst site, the H cluster.
Oxygen permanently binds to hydrogen in the H cluster, shutting down the production of molecular hydrogen (H2). As a result, the hydrogen production is short-lived.
By understanding the mechanism of oxygen’s travel to catalyst site, however, researchers may be able to better devise a blocking mechanism.
Understanding how oxygen reaches the active site will provide insight into how hydrogenase’s oxygen tolerance can be increased through protein engineering, and, in turn, make hydrogenase an economical source of hydrogen fuel.—Klaus Schulten, Swanlund Professor of Physics at Illinois and leader of the Beckman’s Theoretical Biophysics Group
Using computer modeling developed in Schulten’s lab—Nanoscale Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD)—physics doctoral student Jordi Cohen created an all-atom simulation model based on the crystal structure of hydrogenase CpI from Clostridium pasteurianum.
This model allowed Cohen to visualize and track how oxygen and hydrogen travel to the hydrogenase’s catalytic site, where the gases bind, and what routes the molecules take as they exit. Using a new computing concept, he was able to describe gas diffusion through the protein and predict accurately the diffusion paths typically taken.
Although both hydrogen and oxygen diffuse through the protein rather quickly, the model highlighted clear differences.
Oxygen requires a bit more space compared with the lighter and smaller hydrogen, staying close to a few well-localized fluctuating channels. The hydrogen gas traveled more freely. Because the protein is more porous to hydrogen than to oxygen, the hydrogen diffused through the oxygen pathways but also through entirely new pathways closed to oxygen, the researchers discovered.
The researchers concluded that it could be possible to close the oxygen pathways of hydrogenase through genetic modification of the protein and, thereby, increase the tolerance of hydrogenases to oxygen without disrupting the release of hydrogen gas.
Co-authors with Schulten and Cohen were Kwiseon Kim, Paul King and Michael Seibert, all of the National Renewable Energy Laboratory. The National Institutes of Health, National Science Foundation and the U.S. Department of Energy funded the research.
The team detailed their findings in the September issue of the journal Structure.