B01-K02 重田 育照（筑波大学 計算科学研究センター）

B01-K02 重田 育照（筑波大学 計算科学研究センター）

  1. Y. Inoue, Y. Hanazono, K. Noi, A. Kawamoto, M. Kimatsuka, R. Harada, K. Takeda, N. Iwamasa, K. Noguchi, Y. Shigeta, K. Namba, T. Ogura, K. Miki, K. Shinohara, M. Yohda: “Split Conformation of Chaetomium thermophilum Hsp104 Disaggregase” Structure 29, 1-10 (2021) DOI: https://doi.org/10.1016/j.str.2021.02.002
  2. S. Yamazaki, M. Shoji, M. Kayanuma, V. Sladek, D. K. Inaoka, Y. Matsuo, T. Shiba, L. Young, A. L. Moore, K. Kita, Y. Shigeta: “Weak O2 Binding and Strong H2O2 Binding at the Non-heme Diiron Center of Trypanosome Alternative Oxidase”, Boichem. Biophys. Acta Bioenergetics 1826, 148356 (2021) DOI: https://doi.org/10.1016/j.bbabio.2020.148356
  3. S. Fujimura, K. Mio, M. Kuramochi, H. Sekiguchi, K. Ikezaki, M. Mio, Y. Shigeta, T. Kubo, Y. C. Sasaki, “Agonist and Antagonist Diverted Twisting Motions of Single TRPV1 Channel” J. Phys. Chem. B 124, 11617-11624 (2020) DOI: https://doi.org/10.1021/acs.jpcb.0c08250
  4. M. Shoji, T. Murakawa, M. Boero, Y. Shigeta, H. Hayashi, K. Tanizawa, T. Okajima: “Unique Protonation State of the Active Site Aspartate and Topaquinone in Copper Amine Oxidase”, RSC Adv., 10, 38631-38639 (2020) DOI: https://doi.org/10.1039/D0RA06365G
  5. H. Kitoh-Nishioka, Y. Shigeta, K. Ando: “Tunneling Matrix Element and Tunneling Pathways of Protein Electron Transfer Calculated with a Fragment Molecular Orbital Method”, J. Chem. Phys., 153, 104104 (2020) DOI: https://doi.org/10.1063/5.0018423
  6. M. Shoji, K. Abe, M. Boero, Y. Shigeta, Y. Nishiya: “Reaction Mechanism of N-cyclopropylglycine Oxidation by Monomeric Sarcosine Oxidase”, Phys. Chem. Chem. Phys. 22, 16552-16561 (2020) DOI: https://doi.org/10.1039/D0CP01679A
  7. 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”, Proc. Nat. Acad. Sci. U.S.A. 117, 10818-10824 (2020) DOI: https://doi.org/10.1073/pnas.1922538117
  8. B. Nutho, P. Mahalapbutr, K. Hengphasatporn, N. C. Pattaranggoon, N. Simanon, Y. Shigeta, S. Hannongbua, T. Rungrotmongkol: “Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019?: Atomistic Insights into the Inhibitory Mechanisms” Biochemistry 59, 1769-1779 (2020) DOI: https://doi.org/10.1021/acs.biochem.0c00160
  9. H. Shimoyama, Y. Shigeta: “A Free Energy Landscape Analysis of Calmodulin Obtained from an NMR-data Utilized Multi-scale Divide-and-conquer Molecular Dynamics Simulation” Life, 11, 1241 (2021) DOI: https://doi.org/10.3390/life11111241
  10. C. Xie, H. Shimoyama, M. Yamanaka, S. Nagao, H. Komori, N. Shibata, Y. Higuchi, Y. Shigeta, S. Hirota: “Structural and Theoretical Study on Designing Myoglobin to a Domain-swapped Dimer with an Increased Hydrogen Bonding Network at the Hinge Region”, Sci. Adv. 11, 37604-37611 (2021) DOI: https://doi.org/10.1039/d1ra06888a
  11. R. Morita, Y. Shigeta, R. Harada: “Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations”, J. Phys. Chem. B 125, 12712–12717 (2021) DOI: https://doi.org/10.1021/acs.jpcb.1c07928
  12. K. Yanagi, Y. Mitsuta, K. Takaoka, T. Takahashi, K. Hengphasatporn, R. Harada, Y. Shigeta: “Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics Simulations” Chem. Lett. 50, 1964-1967 (2021) DOI: https://doi.org/10.1246/cl.210488
  13. T. Yasuda, R. Morita, Y. Shigeta, R. Harada: “Independent Non-targeted Parallel Cascade Molecular Dynamics (Ino-PaCS-MD) to Enhance Conformational Sampling of Proteins” J. Chem. Theory. Comput. 17, 5933-5943 (2021) DOI: https://doi.org/10.1021/acs.jctc.1c00558
  14. R. Morita, Y. Shigeta, R. Harada: “Comprehensive Predictions of the Secondary Structures for Comparative Analysis in Different Species” J. Struct. Biol. 213, 1077355 (2021) DOI: https://doi.org/10.1016/j.jsb.2021.107735
  15. T. Yasuda, Y. Shigeta, R. Harada: “The Folding of Trp-cage is Regulated by Stochastic Flip of the Sidechain of Tryptophan” Chem. Lett. 50, 162-165 (2021) DOI: https://doi.org/10.1246/cl.200699
  16. R. Morita, Y. Shigeta, R. Harada: “Random Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins” Bull. Chem. Soc. Jpn. 94, 97-105 (2021) DOI: https://doi.org/10.1246/bcsj.20200174
  17. A. Sato, Y. Hori, Y. Shigeta: “Characterization of the Geometrical and Electronic Structures of the Active Site and Its Effects on Surrounding Environment in the Reduced High-potential Iron-sulfur Protein Investigated by Density Functional Theory approach” Inorg. Chem. 62, 2040–2048 (2023) DOI: https://doi.org/10.1021/acs.inorgchem.2c03617
  18. M. Hashimoto, K. Miyagawa, M. Singh, K. Katayama, M. Shoji, Y. Furutani, Y. Shigeta, H. Kandori: “Specific Zinc Binding to Heliorhodopsin” Phys. Chem. Chem. Phys. 25, 3535-3543 (2023) DOI: https://doi.org/10.1039/D2CP04718G
  19. Y. Yamamoto, S. Nakano, Y. Shigeta: “Development Interaction Analysis of Proteins Based on Machine Learning Method and Application to Src Tyrosine Kinase”, Bull. Chem. Soc. Jpn. 96, 42-47(2023) DOI: https://doi.org/10.1246/bcsj.20220304
  20. 【領域内連携】Y. Nishida, S. Yanagisawa, R. Morita, H. Shigematsu, K. Shinzawa-Itoh, H. Yuki, S. Ogasawara, K. Shimizu, T. Iwamoto, C. Nakabayashi, W. Matsumura, H. Kato, C. Gopalasingam, T. Nagao, T. Qaqorh, Y. Takahashi, S. Yamazaki, K. Kamiya, R. Harada, N. Mizuno, H. Takahashi, Y. Akeda, M. Ohnishi, Y. Ishii, T. Kumasaka, T. Murata, K. Muramoto, T. Tosha, Y. Shiro, T. Honma, Y. Shigeta, M. Kubo, S. Takashima, Y. Shintani: “Identifying Antibiotics Based on Structural Differences in the Conserved Allostery from Mitochondrial Heme-copper Oxidases”, Nat. Commun. 13, 7591 (2022) DOI: https://doi.org/10.1038/s41467-022-34771-y
  21. K. Hengphasatporn, R. Harada1, P. Wilasluck, P. Deetanya, E. R. Sukandar, W. Chavasiri, A. Suroengrit, S. Boonyasuppayakorn, T. Rungrotmongkol, K. Wangkanont, Y. Shigeta: “Promising SARS-CoV-2 Main Protease Inhibitor Ligand-binding Modes Evaluated Using LB-PaCS-MD/FMO”Sci. Rep. 12, 17984 (2022) DOI: https://doi.org/10.1038/s41598-022-22703-1
  22. M. Shoji, T. Murakawa, S. Nakanishi, M. Boero, Y. Shigeta, H. Hayashi, T. Okajima, “Peculiar Conformational Change and Electron Transfer realized by the Quinone Cofactor during the Catalytic Cycle of Bacterial Copper Amine Oxidase”, Chem. Sci. 13, 10923-10938 (2022) DOI: https://doi.org/10.1039/D2SC01356H
  23. T. Motoyama, Y. Yamamoto, C. Ishida, F. Hasebe, Y. Shigeta, S. Ito, S. Nakano, “Reaction Mechanism of Ancestral l-Lys α-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis”, ACS Omega, 7, 44407–44419 (2022) DOI: https://doi.org/10.1021/acsomega.2c06334
  24. S. Nagatomo, M. Shoji, T. Terada, K. Nakatani, Y. Shigeta, S. Hirota, S. Yanagisawa, M. Kubo, T. Kitagawa, N. Nagai, M. Ohki, S.-Y. Park, N. Shibayama, “Heme-bound Tyrosine Vibrations in Hemoglobins M Iwate and M Boston: Insight from Resonance Raman Spectroscopy, X-ray Crystallography, and DFT Calculations”, Biophys. J. 121, 2767-2780 (2022) DOI: https://doi.org/10.1016/j.bpj.2022.06.012
  25. T. Yasuda, R. Morita, Y. Shigeta, R. Harada, “Protein Structure Validation Derives the Smart Conformational Search in a Physically Relevant Configurational Subspace”, J. Chem. Inform. Model., 62, 6217-6227 (2022). DOI: https://doi.org/10.1021/acs.jcim.2c01173
  26. H. Aida, Y. Shigeta, R. Harada, “Ligand-binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: ld-PaCS-MD”, Materials 15, 1490 (2022). DOI: https://doi.org/10.3390/ma15041490
  27. Y. Munei, K. Hengphasatporn, Y. Hori, R. Harada, Y. Shigeta, “Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses”, J. Agricultural Food Chem., 71, 9528–9537 (2023) DOI: https://doi.org/10.1021/acs.jafc.3c01253
  28. Y. Yamamoto, Y. 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”, Chem. Lett. 52, 120-123 (2023). DOI: https://doi.org/10.1246/cl.220503
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