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

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