A Water Dimer Shift Activates a Proton Pumping Pathway in the P R → F Transition of ba 3 Cytochrome c Oxidase.

Broken-symmetry density functional calculations have been performed on the [Fea3 4+ ,CuB 2+ ] state of the dinuclear center (DNC) for the PR → F part of the catalytic cycle of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H2 O molecules in the DNC affects the pKa values of the residue side chains of Tyr237 and His376+ , which are crucial for proton transfer/pumping in ba3 CcO from Tt. The calculated lowest energy structure of the DNC in the [Fea3 4+ ,CuB 2+ ] state (state F) is of the form Fea3 4+ ═O2- ···CuB 2+ , in which the H2 O ligand that resulted from protonation of the OH- ligand in the PR state is dissociated from the CuB 2+ site. The calculated Fea3 4+ ═O2- distance in F (1.68 Å) is 0.03 Å longer than that in PR (1.65 Å), which can explain the different Fea3 4+ ═O2- stretching modes in P (804 cm-1 ) and F (785 cm-1 ) identified by resonance Raman experiments. In this F state, the CuB 2+ ···O2- (ferryl-oxygen) distance is only around 2.4 Å. Hence, the subsequent OH state [Fea3 3+ -OH- -CuB 2+ ] with a μ-hydroxo bridge can be easily formed, as shown by our calculations.