B01：Quantum Bioenergetics for Exploring Dynamics of Metals in Protein
Yasuteru SHIGETA
（Center for Computational Sciences, University of Tsukuba）
Lab website
The dynamism of biological systems lies in the various conversion mechanisms interwoven with proteins, nucleic acids, and other biological molecules. For example, synthetic and decomposing enzymes mutually convert substances, photosynthetic systems and respiratory chains mutually convert energy and substances, and also convert the existence and concentration of substances into information and transmit it. These understandings are not only important for exploring the fundamentals of life phenomena, but also essential information in creating novel artificial transformation systems. In particular, various transition metal ions are involved when the energy conversion system are expressed in biological system. We believe that their unique electronic degrees of freedom (charge and spin) and changes in geometrical structure are the keys for regulating the precise biological functions. In order to understand the underlying physicochemical mechanisms, we have been conducting theoretical studies using first-principles calculations based on quantum theory. Specifically, we performed QM/MM-based electronic structure analyses of multiple Fe and Cu-containing systems, including cytochrome c oxidase, photosystem II, nitrilehydratase, bilirubin oxidase, and hydrogenase, to analyze reaction mechanisms and properties.
Major publications
T. Murakawa, K. Kurihara, M. Shoji, C. Shibazaki, T. Sunami, T. Tamada, N. Yano, T. Yamada, K. Kusaka, M. Suzuki, Y. Shigeta, R. Kuroki, H. Hayashi, T. Yano, K. Tanizawa, M. Adachi, T. Okajima
“Neutron crystallography of copper amine oxidase reveals a keto form cofactor and proton sharing”
Proceedings of National Academy of Science U.S.A., 2020, accepted
doi:
H. Kitoh-Nishioka, Y. Shigeta, S. Ito, A. Kimura
“Excitonic Couplings in Heliobacterial Type I Homodimeric Reaction Center”
Journal of Physical Chemistry B, 2020, 124, 389-403
doi: 10.1021/acs.jpcb.9b11290
M. Akter, T. Tokiwa, M. Shoji, K. Nishikawa, Y. Shigeta, T. Sakurai, K. Kataoka, Y. Higuchi, N. Shibata
“Redox potential-dependent formation of an unusual His–Trp bond in bilirubin oxidase”
Chemistry-A European Journal, 2018, 24, 18052-18058
doi: 10.1002/chem.201803798
M. Kayanuma, M. Shoji, M. Yoda, M. Odaka, Y. Shigeta
“Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study”
Journal of Physical Chemistry B, 2016, 120, 3259–3266
doi: 10.1021/acs.jpcb.5b11363
K. Kamiya, Y. Shigeta
“First-principles Molecular Dynamics Studies on the Atomistic Behavior of His503 in Bovine Cytochrome c Oxidas”
Biochimica et Biophysica Acta, 2011, 1807, 1328-1335
doi: 10.1016/j.bbabio.2011.03.015