XVIth International Workshop on
Quantum Systems in
Chemistry and Physics
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Origin of the variety of the Cu2S2 core structure of the CuA sites: a density functional theory study
Orio Okuyama1, Yasuteru Shigeta1,2, Haruki Nakamura1, and Yu Takano1

1Institute for Protein Research, Osaka University, Japan
2Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Japan
The CuA site, a proximate electron-transfer intermediate from an electron source, is contained both in cytochrome c oxidase (C cO), the terminal electron acceptor in aerobic respiration, and in nitrous oxide reductase (N2OR), the terminal acceptor in anaerobic respiration. The CuA site is a binuclear copper site with two bridging cystenyl thiolate groups. Each copper ion is coordinated by a histidine side chain and a methionine side chain or a carbonyl oxygen of the backbone.
Spectroscopic studies have suggested the σu* ground state of the oxidized CuA site is due to the direct CuCu interaction, facilitating a rapid electron transfer over long distances with low driving forces. We have shown that the ground state of the Cu2S2 core is the πu state even with a shorter CuCu distance in the oxidized state, and that a combination of electrostatic and orbital interactions is required to stabilized the σu* state of the Cu2S2 core rather than the πu state [1].
High resolution X-ray crystal structures of the CuA sites in several proteins have so far been reported. The three-dimensional structures of the Cu2S2 core of the CuA sites show various CuCu or SS distances, 2.352.59 Å for the CuCu distance and 3.764.24 Å for the SS distance. In order to elucidate the origin of the variety of the Cu2S2 core structure of several CuA sites, we have examined electronic structures of the Cu2S2 core of the CuA sites, using the density functional theory (DFT) with Gaussian09 program.
We built models from 10 types of C cO (PDB ID: 1V54, 1V55, 2CUA, 2GSM, 2DYR, 2EIJ, 3ABK, 3ABM, 3AG2, 3AG3), 3 types of N2OR (PDB ID: 1FWX, 2IWF, 2IWK), and an engineered CuA azurin (PDB ID: 1CC3). DFT calculations were performed using the exchange-correlation functional, M06, because the M06 functional reproduces the energy difference of the Cu2S2 core between the σu* and πu states at the CCSD(T) level of theory. Wachters+f basis set was used for copper ions and the other atoms were treated with 6-311G++(df,pd) basis set.

[1] Y. Takano, Y. Shigeta, K. Koizumi, H. Nakamura, Int. J. Quantum Chem. in press.


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