A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus

Broken-symmetry density functional calculations have been performed on the [Fe-a3, Cu-B] dinuclear center (DNC) of ba(3) cytochrome c oxidase from Thermus thermophilus in the states of [Fea(3)(3+)-(HO2) - Cu-B(2+), Tyr237(-)] and [Fe-a3(4+) = O2-, OH--Cu-B(2+), Tyr237(center dot)], using both PW91-D3 and OLYP-D3 functionals. Tyr237 is a special tyrosine cross-linked to His233, a ligand of Cu-B. The calculations have shown that the DNC in these states strongly favors the protonation of His376, which is above propionate-A, but not of the carboxylate group of propionate-A. The energies of the structures obtained by constrained geometry optimizations along the O-O bond cleavage pathway between [Fe-a3(3+)-(O-OH)(-)-Cu-B(2+), Tyr237(-)] and [Fe-a3(4+)=O2-center dot center dot center dot HO--Cu-B(2+), Tyr237(center dot)] have also been calculated. The transition of [Fe-a3(3+)=(O-OH)(-)-Cu-B(2+), Tyr237(center dot)] -> [Fe-a3(4+)=O2-center dot center dot center dot HO--Cu-B(2+), Tyr237(center dot)] shows a very small barrier, which is less than 3.0/2.0 kcal mol(-1) in PW91-D3/OLYP-D3 calculations. The protonation state of His376 does not affect this O-O cleavage barrier. The rate limiting step of the transition from state A (in which O-2 binds to Fe-a3(2+)) to state P-M ([Fe-a3(4+)=O2-, OH--Cu-B(2+), Tyr237(center dot)], where the O-O bond is cleaved) in the catalytic cycle is, therefore, the proton transfer originating from Tyr237 to O-O to form the hydroperoxo [Fe-a3(3+)-(O-OH)(-)-Cu-B(2+), Tyr237(-)] state. The importance of His376 in proton uptake and the function of propionate-A/neutralAsp372 as a gate to prevent the proton from back-flowing to the DNC are also shown.