原著論文
・NMR detection of hydrogen bond network in a proton pump rhodopsin RxR and its alteration during the cyclic photoreaction
S. Kori, Y. Shibahashi, T. Ekimoto, A. Nishiyama, S. Yoshimi, K. Yamaguchi, S. Nagatoishi, M. Ohta, K. Tsumoto, M. Nakanishi, PA Defossez, M. Ikeguchi, *K. Arita, J. Am. Chem. Soc. , in press(2023)

・Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding
Y. Kurihara, T. Ekimoto, Christopher T Gordon, Y. Uchijima, R. Sugiyama, T. Kitazawa, A. Iwase, R. Kotani, R. Asai, V. Pingault, M. Ikeguchi, J. Amiel, *H. Kurihara, J.Clin. Invest. , 133, e151536 (2023), DOI: 10.1172/JCI151536

・TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction
K. Sakaniwa, A. Fujimura, T. Shibata, H. Shigematsu, T. Ekimoto, M. Yamamoto, M. Ikeguchi, K. Miyake, U. Ohto, *T. Shimizu, Nat. Commun. , 14, 164 (2023), DOI: 10.1038/s41467-023-35844-2

・Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1
S. Kori, Y. Shibahashi, T. Ekimoto, A. Nishiyama, S. Yoshimi, K. Yamaguchi, S. Nagatoishi, M. Ohta, K. Tsumoto, M. Nakanishi, PA Defossez, M. Ikeguchi, *K. Arita, Bioorg. Med. Chem. , 52, 116500 (2021), DOI: 10.1021/acs.jcim.1c00389

・Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease
*K. Moritsugu, T. Ekimoto, M. Ikeguchi, J. Chem. Inf. Model , 63, 240-250 (2022), DOI: 10.1021/acs.jcim.2c00946.

・Development of the force field for cyclosporine A
T. Yamane, T. Ekimoto, *M. Ikeguchi, Biophys. Physicobiol. , 19, e190045 (2022), DOI: 10.2142/biophysico.bppb-v19.0045

・Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D
T. Tanaka, T. Ekimoto, M. Nagatomo, M. Neyazaki, E. Shimoji, T. Yamane, S. Kanagawa, R. Oi, E. Mihara, J. Takagi, S. Akashi, *M. Ikeguchi, *T. Nogi, ProteinSci. , 31, e4452 (2022), DOI: 10.1002/pro.4452

・gr Predictor: A Deep-Learning Model for Predicting the Hydration Structures around Proteins
K. Kawama, Y. Fukushima, M. Ikeguchi, M. Ohta, and *T. Yoshidome, J Chem Inf Model., 62, 4460-4473 (2022), DOI: 10.1021/acs.jcim.2c00987

・3D-RISM-AI: A Machine Learning Approach to Predict Protein-Ligand Binding Affinity Using 3D-RISM
K. Osaki, T. Ekimoto, T. Yamane, *M. Ikeguchi, J.Phys. Chem. B., 126,6148-6158 (2022), DOI: 10.1021/acs.jpcb.2c03384

・Structure of SARS-CoV-2 membrane protein essential for virus assembly
Z. Zhang, N. Nomura, Y. Muramoto, T. Ekimoto, T. Uemura, K. Liu, M. Yui, N. Kono, J. Aoki, M. Ikeguchi, T. Noda, S. Iwata, U. Ohto, *T. Shimizu, Nat. Commun., 13,4399 (2022) DOI: 10.1038/s41467-022-32019-3

・Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane
K. Sato, R. Sasaki, R. Matsuda, M. Nakagawa, T. Ekimoto, T. Yamane, M. Ikeguchi, K. V. Tabata, H. Noji, *K. Kinbara, J. Am. Chem. Soc., 144,11802-11809 (2022), DOI: 10.1021/jacs.2c04118

・Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1
S. Kori, Y. Shibahashi, T. Ekimoto, A. Nishiyama, S. Yoshimi, K. Yamaguchi, S. Nagatoishi, M. Ohta, K. Tsumoto, M. Nakanishi, PA Defossez, M. Ikeguchi, *K. Arita, Bioorg. Med. Chem. , 52, 116500 (2021), DOI: 10.1021/acs.jcim.1c00389

・Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble
A. Kidera, K. Moritsugu, T. Ekimoto, *M. Ikeguchi, J. Mol. Biol. , 433, 167324 (2021), DOI: 10.1021/acs.jcim.1c00389

・Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations
T. Ekimoto, T. Kudo, T. Yamane, * M. Ikeguchi, J. Chem. Inf. Model , 61, 3625–3637 (2021), DOI: 10.1021/acs.jcim.1c00534

・Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Recepto
K. Takedomi, M. Ohta, T. Ekimoto, * M. Ikeguchi, J. Chem. Inf. Model , 61, 3583–3592 (2021), DOI: 10.1021/acs.jcim.1c00389

・Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion
R. Tamura-Sakaguchi, R. Aruga, M. Hirose, T. Ekimoto, T. Miyake, Y. Hizukuri, R. Oi, M. K. Kaneko, Y. Kato, Y. Akiyama, M. Ikeguchi, K. Iwasaki, *T. Nogi, Acta. Crystallogr. D Struct. Biol. , 77, 645–662 (2021), DOI: 10.1021/acs.jcim.1c00534

・Structural and dynamical insights into the PH domain of p62 in human TFIIH
M. Okuda, T. Ekimoto, J. Kurita, M. Ikeguchi, *Y. Nishimura, Nucleic Acids Research , 49, 2916–2930 (2021), DOI: 10.1093/nar/gkaa1045

・Imidazolinium‐based Multiblock Amphiphile as Transmembrane Anion Transporter
M. Mori, K. Sato, T. Ekimoto, S. Okumura, M. Ikeguchi, K. V. Tabata, H. Noji, *K. Kinbara, Chem. Asian J. , 16, 147-157 (2020), DOI: 10.1002/asia.202001106

・A synthetic ion channel with anisotropic ligand response
*T. Muraoka, D. Noguchi, R. S. Kasai, K. Sato, R. Sasaki, K. V. Tabata, T. Ekimoto, M. Ikeguchi, K. Kamagata, N. Hoshino, H. Noji, T. Akutagawa, K. Ichimura, *K. Kinbara, Nat. Commun. , 11, 2924 (2020), DOI: 10.1002/open.201900374

・Revisiting biomolecular NMR spectroscopy for promoting small-molecule drug discovery
*H. Hanzawa, T. Shimada, M. Takahashi, H. Takahashi, Journal of Biomolecular NMR , 74, 501–508 (2020), DOI: 10.1007/s10858-020-00314-0

・Cooperative interactions facilitate stimulation of Rad51 by the Swi5-Sfr1 auxiliary factor complex
B. Argunhan, M. Sakakura, N. Afshar, M. Kurihara, K. Ito, T. Maki, S. Kanamaru, Y. Murayama, H. Tsubouchi, M. Takahashi, *H. Takahashi and *H. Iwasaki, eLife, 9, e52566 (2020), DOI: 10.7554/eLife.52566

・Hydration properties of a protein at low and high pressures: Physics of pressure denaturation
M. Inoue, T. Hayashi, S. Hikiri, M. Ikeguchi, *M. Kinoshita, J. Chem. Phys., 152, 065103 (2020), DOI: 10.1063/1.5140499

・Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments
T. Ekimoto, Y. Kokabu, T. Oroguchi, *M. Ikeguchi, Biophys. Physicobiol., 16, 377-390 (2019), DOI: 10.2142/biophysico.16.0_377

・Structural mechanisms underlying activity changes in an AMPA-type glutamate receptor induced by substitutions in its ligand-binding domain
*M. Sakakura, Y. Ohkubo, H. Oshima, S. Re, M. Ito, Y. Sugita, and *H. Takahashi, Structure, 27, 1698-1709 (2019), DOI: 10.1016/j.str.2019.09.004

・How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2?
T. Yamada, T. Hayashi, S. Hikiri, N. Kobayashi, H. Yanagawa, M. Ikeguchi, M. Katahira,, T. Nagata, *M. Kinoshita, J. Chem. Inf. Model., 59, 3533-3544 (2019), DOI: 10.1021/acs.jcim.9b00226

・An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins
S. Hikiri, T. Hayashi, M. Inoue, T. Ekimoto, M. Ikeguchi, *M. Kinoshita, J. Chem. Phys., 150, 175101 (2019), DOI: 10.1063/1.5093110

・Population shift mechanism for partial agonism of AMPA receptor
H. Oshima, Suyong Re, M. Sakakura, H. Takahashi, *Y. Sugita, Biophys. J.,116, 57-68 (2019), DOI: 10.1016/j.bpj.2018.11.3122

・Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method
T. Ekimoto, T. Yamane, *M. Ikeguchi,J. Chem. Theory Comput., 14, 6544-6559 (2018), DOI: 10.1021/acs.jctc.8b00280

・Statistical thermodynamics for the unexpectedly large difference between disaccharide stereoisomers in terms of solubility in water
S. Hikiri, T. Hayashi, M. Ikeguchi, *M. Kinoshita, Phys. Chem. Chem. Phys.,20, 23684-23693 (2018), DOI: 10.1039/c8cp04377a

書籍/総説・解説
・“Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses”
Abhishek Singharoy*, Chris Chipot, Toru Ekimoto, Kano Suzuki, Mitsunori Ikeguchi, Ichiro Yamato,
Takeshi Murata*, Front. Physiol., 10 , 1-12 (2019), DOI: 10.3389/fphys.2019.00046

・「Integrative Structural Biology with Hybrid Methods」,
Nakamura H, Kleywegt G, Burley K.S, Markley L. J.,
“Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle
X-Ray Scattering Data”, T. Ekimoto, *M. Ikeguchi,
Springer Nature Singapore (2018), 237-258, ISBN:978-981-13-2199-3