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Open AccessArticle

Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction

1
Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
2
Department of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
3
Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
4
Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, 84538 Bratislava, Slovakia
5
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
6
Graduate School of Natural Science & Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
*
Authors to whom correspondence should be addressed.
Academic Editors: Yasutaka Kitagawa, Ryohei Kishi and Masayoshi Nakano
Molecules 2019, 24(1), 76; https://doi.org/10.3390/molecules24010076
Received: 20 November 2018 / Revised: 17 December 2018 / Accepted: 20 December 2018 / Published: 26 December 2018
(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)
Geometric and electronic structure changes in the copper (Cu) centers in bilirubin oxidase (BOD) upon a four-electron reduction were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. For the QM region, the unrestricted density functional theory (UDFT) method was adopted for the open-shell system. We found new candidates of the native intermediate (NI, intermediate II) and the resting oxidized (RO) states, i.e., NIH+ and RO0. Elongations of the Cu-Cu atomic distances for the trinuclear Cu center (TNC) and very small structural changes around the type I Cu (T1Cu) were calculated as the results of a four-electron reduction. The QM/MM optimized structures are in good agreement with recent high-resolution X-ray structures. As the structural change in the TNC upon reduction was revealed to be the change in the size of the triangle spanned by the three Cu atoms of TNC, we introduced a new index (l) to characterize the specific structural change. Not only the wild-type, but also the M467Q, which mutates the amino acid residue coordinating T1Cu, were precisely analyzed in terms of their molecular orbital levels, and the optimized redox potential of T1Cu was theoretically reconfirmed. View Full-Text
Keywords: catalytic intermediate; protonation; Cu oxidation state; X-ray reduction; SONO; molecular orbital analysis catalytic intermediate; protonation; Cu oxidation state; X-ray reduction; SONO; molecular orbital analysis
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MDPI and ACS Style

Tokiwa, T.; Shoji, M.; Sladek, V.; Shibata, N.; Higuchi, Y.; Kataoka, K.; Sakurai, T.; Shigeta, Y.; Misaizu, F. Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction. Molecules 2019, 24, 76.

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