TCB Publications - Abstract
Ivo Hofacker and Klaus Schulten. Oxygen and proton pathways in cytochrome c oxidase. PROTEINS: Structure, Function, and Genetics, 30:100-107, 1998.
Results: Molecular dynamics simulations of oxygen diffusion through the protein reveal a pathway to the oxygen binding site starting at a hydrophobic cavity near the membrane exposed surface of subunit I, close to the interface to subunit III. A large number of water sites is predicted within the protein. The water molecules form two channels along which protons can enter from the cytoplasmic (matrix) side of the protein and reach the binuclear center.
Conclusions: Oxygen is channeled to the catalytic center of the enzyme along a well defined path. Hydrophobic cavities at the start of the path could serve as reservoirs for oxygen. Water might play an essential role for the transfer of protons in cytochrome c oxidase. A possible pumping mechanism is proposed that involves a shuttling motion of a glutamic acid side chain, which could then transfer a proton to a propionate group of heme
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