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Acknowledgements
I would like to take this opportunity to express my best gratitude to Professor Yasuteru
Shigeta and Associate professor Ryuhei Harada for their assistance throughout my doctoral
studies. I also acknowledge the collaborators, Prof. Hiroaki Tokiwa, Prof. Makoto Takeda,
Prof. Hitoshi Shimano, Associate Prof. Shogo Nakano, Associate Prof. Takashi Ikawa and Dr.
Vladimir Sladek for their assistance throughout my doctoral studies.
110
Publication List
◎: Doctoral thesis’s paper, 〇: First author.
・Konishi, H.; Matsubara, M.; Mori, K.; Tokiwa, T.; Arulmozhiraja, S.; Yamamoto, Y.;
Ishikawa, Y.; Hashimoto, H.; Shigeta, Y.; Tokiwa, H.; Manabe, K., Mechanistic Insight into
Weak Base-Catalyzed Generation of Carbon Monoxide from Phenyl Formate and Its
Application to Catalytic Carbonylation at Room Temperature without Use of External Carbon
Monoxide Gas. Advanced Synthesis & Catalysis 2017, 359 (20), 3592-3601.
・Motoyama, T.; Nakano, S.; Yamamoto, Y.; Tokiwa, H.; Asano, Y.; Ito, S., Product Release
Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase.
Biochemistry 2017, 56 (43), 5758-5770.
・ Akai, S.; Ikawa, T.; Kaneko, H.; Yamamoto, Y.; Arulmozhiraja, S.; Tokiwa, H.,
3-(Triflyloxy)benzynes Enable the Regiocontrolled Cycloaddition of Cyclic Ureas to
Synthesize 1,4-Benzodiazepine Derivatives. Synlett 2018, 29 (07), 943-948.
◎ Yamamoto, Y.; Takei, K.; Arulmozhiraja, S.; Sladek, V.; Matsuo, N.; Han, S. I.; Matsuzaka,
T.; Sekiya, M.; Tokiwa, T.; Shoji, M.; Shigeta, Y.; Nakagawa, Y.; Tokiwa, H.; Shimano, H.,
Molecular association model of PPARalpha and its new specific and efficient ligand,
pemafibrate: Structural basis for SPPARMalpha. Biochem Biophys Res Commun 2018, 499
(2), 239-245.
・Tokiwa, T.; Nakano, S.; Yamamoto, Y.; Ishikawa, T.; Ito, S.; Sladek, V.; Fukuzawa, K.;
Mochizuki, Y.; Tokiwa, H.; Misaizu, F.; Shigeta, Y., Development of an Analysis Toolkit,
AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital
Calculations. Journal of Chemical Information and Modeling 2018, 59(1), 25-30.
・Matsuzaka, T.; Kuba, M.; Koyasu, S.; Yamamoto, Y.; Motomura, K.; Arulmozhiraja, S.;
Ohno, H.; Sharma, R.; Shimura, T.; Okajima, Y.; Han, S.-i.; Aita, Y.; Mizunoe, Y.; Osaki, Y.;
111
Iwasaki, H.; Yatoh, S.; Suzuki, H.; Sone, H.; Takeuchi, Y.; Yahagi, N.; Miyamoto, T.; Sekiya,
M.; Nakagawa, Y.; Ema, M.; Takahashi, S.; Tokiwa, H.; Shimano, H., Hepatocyte Elovl6
determines ceramide acyl-chain length and hepatic insulin sensitivity in mice. Hepatology
2019, doi.org/10.1002/hep.30953.
・Kawasaki, M.; Kambe, A.; Yamamoto, Y.; Arulmozhiraja, S.; Ito, S.; Nakagawa, Y.; Tokiwa,
H.; Nakano, S.; Shimano, H., Elucidation of Molecular Mechanism of a Selective PPARalpha
Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography,
Thermodynamic Analysis, and First-Principle Calculations. Int J Mol Sci 2020, 21 (1).
・Takeda, M.; Seki, F.; Yamamoto, Y.; Nao, N.; Tokiwa, H., Animal morbilliviruses and their
cross-species transmission potential. Curr Opin Virol 2020, 41, 38-45.
・Seki, F.; Yamamoto, Y.; Fukuhara, H.; Ohishi, K.; Maruyama, T.; Maenaka, K.; Tokiwa, H.;
Takeda, M., Measles Virus Hemagglutinin Protein Establishes a Specific Interaction With the
Extreme N-Terminal Region of Human Signaling Lymphocytic Activation Molecule to
Enhance Infection. Front Microbiol 2020, 11, 1830.
◎ Yamamoto, Y.; Nakano, S.; Seki, F.; Shigeta, Y.; Ito, S.; Tokiwa, H.; Takeda, M.,
Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the
Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with
Canine Distemper Virus. Molecules 2021, 26 (5), 1262.
〇 Ikawa, T.; Yamamoto, Y.; Heguri, A.; Fukumoto, Y.; Murakami, T.; Takagi, A.; Masuda,
Y.; Yahata, K.; Aoyama, H.; Shigeta, Y.; Tokiwa, H.; Akai, S., Could London Dispersion
Force Control Regioselective (2 + 2) Cyclodimerizations of Benzynes? YES: Application to
the Synthesis of Helical Biphenylenes. Journal of the American Chemical Society 2021, 143
(29), 10853-10859.
・Sladek, V.; Yamamoto, Y.; Harada, R.; Shoji, M.; Shigeta, Y.; Sladek, V., pyProGA—A
PyMOL plugin for protein residue network analysis. PLOS ONE 2021, 16 (7), e0255167.
〇 Yuta Yamamoto, Tomoharu Motoyama, Chiharu Ishida, Fumihito Hasebe, Yasuteru
112
Shigeta, Sohei Ito and Shogo Nakano, Biochemical and structural analysis of bona fide
ancestral L-Lys a-oxidase to predict molecular evolution of substrate specificity. ACS Omega
2022, 7 (48), 44407-44419.
◎ Yuta Yamamoto, Shogo Nakano and Yasuteru Shigeta, Dynamical interaction analysis of
proteins by a random forest-fragment molecular orbital (RF-FMO) method and application to
Src
tyrosine
kinase.
Bulletin
of
the
Chemical
Society
of
Japan
2023,
doi.org/10.1246/bcsj.20220304.
◎ Yuta Yamamoto and Yasuteru Shigeta, Theoretical Study on the Regulating Mechanism of
the Transition Between the Open-closed State of hCtBP2: A Combined Molecular Dynamics
and Quantum Mechanical Interaction Analysis. Chemistry Letters 2023, Accepted.
113
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