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

• Published in: Physical chemistry chemical physics : PCCP 2020-12, Vol.22 (46), p.26652-26668
• Main Authors: Noodleman, Louis, Han Du, Wen-Ge, McRee, Duncan, Chen, Ying, Goh, Teffanie, Götz, Andreas W
• Format: Article
• ISSN: 1463-9076; 1463-9084
• DOI: 10.1039/d0cp04848h

After a general introduction to the features and mechanisms of cytochrome c oxidases (C c Os) in mitochondria and aerobic bacteria, we present DFT calculated physical and spectroscopic properties for the catalytic reaction cycle compared with experimental observations in bacterial ba 3 type C c O, also with comparisons/contrasts to aa 3 type C c Os. The Dinuclear Complex (DNC) is the active catalytic reaction center, containing a heme a 3 Fe center and a near lying Cu center (called Cu B ) where by successive reduction and protonation, molecular O 2 is transformed to two H 2 O molecules, and protons are pumped from an inner region across the membrane to an outer region by transit through the C c O 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 C c O 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 p K 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. DFT calculated structures, vibrational frequencies, and energies provide insights into the reaction/proton pumping cycle of cytochrome c oxidase.