The CUₐ center of cytochrome oxidase : electronic structure calculations and electron-tunneling pathways

Citation

Ramirez, Benjamin E. (1998) The CUₐ center of cytochrome oxidase : electronic structure calculations and electron-tunneling pathways. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/r7t8-xt78. https://resolver.caltech.edu/CaltechTHESIS:11132009-113407018

Abstract

The Cu_A center is a mixed valence, dithoilate-bridged, binuclear copper center that is found in cytochrome oxidase. It serves as the initial acceptor of electrons from cytochrome c. The Cu_A center has distinct UV/Vis and EPR spectroscopic features. It is likely that this site has an extremely low inner-sphere reorganization energy because it very efficiently transfer electrons st low reaction driving forces over long distances (~15-20 Å) in less than a millisecond. We undertook DFT calculations on a Cu_A model complex to examine the structure, spectroscopic assignments and reorganization energy of the center. The optimized structure of the Cu_A model complex closely resembles the structure determined from x-ray diffraction studies. The rms overlap of the optimized structure with the structure derived from EXAFS data is 0.16 Å. Based on the calculated MO diagram, we assign the bands in the UV/Vis absorption spectrum to transitions originating from lower lying doubly-filled orbitals into a σ_(Cu)* singly-occupied HOMO that is primarily Cu d_(x2-y2)/S p_x in character. We find that the character of the HOMO as well as the transition energies and intensities are extremely sensitive to the Cu-S-Cu angle. We also calculated the optimized structure of the reduced center to examine the role of the protein in reducing the inner-sphere reorganization energy. The following picture emerges from the calculations of the coordination geometry: the protein framework imposes a structure, with a low dielectric cavity in which the trigonal geometry of the oxidized form is optimal. In addition, this framework prevents the reduced structure from distorting to its optimal (linear, two-coordinate) structure. This so-called rack effect of the folded protein enables Cu_A and blue copper centers to function as very efficient electron-transfer agents.

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