Coupled transport of electrons and protons in a bacterial cytochrome c oxidase—DFT calculated properties compared to structures and spectroscopies

Abstract

After a general introduction to the features and mechanisms of cytochrome c oxidases (CcOs) in mitochondria and aerobic bacteria, we present DFT calculated physical and spectroscopic properties for the catalytic reaction cycle compared with experimental observations in bacterial ba₃ type CcO, also with comparisons/contrasts to aa₃ type CcOs. The Dinuclear Complex (DNC) is the active catalytic reaction center, containing a heme a₃ Fe center and a near lying Cu center (called Cu_B) where by successive reduction and protonation, molecular O₂ is transformed to two H₂O molecules, and protons are pumped from an inner region across the membrane to an outer region by transit through the CcO integral membrane protein. Structures, energies and vibrational frequencies for Fe–O and O–O modes are calculated by DFT over the catalytic cycle. The calculated DFT frequencies in the DNC of CcO are compared with measured frequencies from Resonance Raman spectroscopy to clarify the composition, geometry, and electronic structures of different intermediates through the reaction cycle, and to trace reaction pathways. X-ray structures of the resting oxidized state are analyzed with reference to the known experimental reaction chemistry and using DFT calculated structures in fitting observed electron density maps. Our calculations lead to a new proposed reaction pathway for coupling the P_R → F → O_H (ferryl-oxo → ferric-hydroxo) pathway to proton pumping by a water shift mechanism. Through this arc of the catalytic cycle, major shifts in pK_a's of the special tyrosine and a histidine near the upper water pool activate proton transfer. Additional mechanisms for proton pumping are explored, and the role of the Cu_B⁺ (cuprous state) in controlling access to the dinuclear reaction site is proposed.