Mobility of Xe Atoms within the Oxygen Diffusion Channel of Cytochrome ba3 Oxidase

We use a form of freeze-trap, kinetic crystallography to explore the migration of Xe atoms away from the dinuclear heme a(3)/Cu-B center in Thermus thermophilus cytochrome ba(3) oxidase. This enzyme is a member of the heme-copper oxidase superfamily and is thus crucial for dioxygen-dependent life. The mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. Pressurization of crystals with Xe gas previously revealed a O-2 diffusion channel in cytochrome ba(3) oxidase that is continuous, Y-shaped, 18-20 angstrom in length and comprised of hydrophobic residues, connecting the protein surface within the bilayer to the a(3)-Cu-B center in the active site. To understand movement of gas molecules within the O-2 channel, we performed crystallographic analysis of 19 Xe laden crystals freeze-trapped in liquid nitrogen at selected times between 0 and 480 s while undergoing outgassing at room temperature. Variation in Xe crystallographic occupancy at five discrete sites as a function of time leads to a kinetic model revealing relative degrees of mobility of Xe atoms within the channel. Xe egress occurs primarily through the channel formed by the Xe1 -> Xe5 -> Xe3 -> Xe4 sites, suggesting that ingress of O-2 is likely to occur by the reverse of this process. The channel itself appears not to undergo significant structural changes during Xe migration, thereby indicating a passive role in this important physiological function.