made with VMD
In an optimistic future, cars and appliances will be powered by renewable energy produced by burning hydrogen gas, with water being the only waste product. To supply this hydrogen gas, scientists are turning their attention to an enzyme called hydrogenase that is found in certain microorganisms, which produce hydrogen gas from sunlight and water. This enzyme, however, is sensitive to oxygen gas, which irreversibly deactivates its hydrogen-producing active site. 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. In a recent paper (also described in this webpage), the programs NAMD and VMD are used to analyze the gas diffusion process inside hydrogenase, and how it correlates with the protein's internal fluctuations, thereby creating a map of the oxygen pathways. The calculations revealed two distinct pathways for oxygen to reach the active site. Gases participate in physiological processes of many organisms and the new computational strategy developed promises to image gas diffusion pathways for many relevant proteins. In fact, the researchers are currently inspecting hundreds of proteins for their ability to internally transport gas molecules.