Structural Analysis and Molecular Dynamics Simulations of Urease From Ureaplasma parvum 査読

Heng Ning Wu, Junso Fujita, Yukiko Nakura, Masao Inoue, Koichiro Suzuki, Toru Ekimoto, Bingjie Yin, Yohta Fukuda, Kazuo Harada, Tsuyoshi Inoue, Mitsunori Ikeguchi, Keiichi Namba, Itaru Yanagihara

Journal of Molecular Biology   437 ( 21 )   169368 - 169368   2025年11月（ ISSN:0022-2836 ）

Narrowed pore conformations of aquaglyceroporins AQP3 and GlpF. 査読

Kozai D, Inoue M, Suzuki S, Kamegawa A, Nishikawa K, Suzuki H, Ekimoto T, Ikeguchi M, Fujiyoshi Y

Nature communications   16 ( 1 )   2653   2025年03月

Ureaplasma parvum由来ウレアーゼの構造解析と分子ダイナミックシミュレーション

呉 恒寧, 藤田 純三, 名倉 由起子, 井上 雅郎, 鈴木 孝一朗, 浴本 亨, 池口 満徳, 難波 啓一, 柳原 格

日本マイコプラズマ学会雑誌   ( 51 )   17 - 19   2025年03月（ ISSN:1340-2382 ）

Synergistic Activation of TLR7 and 8 Mediated by Reduction of Electrostatic Repulsion.

Ekimoto T, Nomura M, Saito Y, Suzuki M, Yamane T, Zhang Z, Ohto U, Ikeguchi M, Shimizu T

Chemical & pharmaceutical bulletin   72 ( 11 )   1005 - 1013   2024年11月（ ISSN:0009-2363 ） （ eISSN:1347-5223 ）

静電反発力の減少が介在するTLR7とTLR8の相乗的活性化(Synergistic Activation of TLR7 and 8 Mediated by Reduction of Electrostatic Repulsion)

Ekimoto Toru, Nomura Masami, Saito Yuri, Suzuki Minami, Yamane Tsutomu, Zhang Zhikuan, Ohto Umeharu, Ikeguchi Mitsunori, Shimizu Toshiyuki

Chemical & Pharmaceutical Bulletin   72 ( 11 )   1005 - 1013   2024年11月（ ISSN:0009-2363 ）

Structural basis for hepatitis B virus restriction by a viral receptor homologue.

Shionoya K, Park JH, Ekimoto T, Takeuchi JS, Mifune J, Morita T, Ishimoto N, Umezawa H, Yamamoto K, Kobayashi C, Kusunoki A, Nomura N, Iwata S, Muramatsu M, Tame JRH, Ikeguchi M, Park SY, Watashi K

Nature communications   15 ( 1 )   9241   2024年10月（ eISSN:2041-1723 ）

Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase. 査読

Araki M, Ekimoto T, Takemura K, Matsumoto S, Tamura Y, Kokubo H, Bekker GJ, Yamane T, Isaka Y, Sagae Y, Kamiya N, Ikeguchi M, Okuno Y

Journal of the American Chemical Society   146 ( 42 )   28685 - 28695   2024年10月（ ISSN:0002-7863 ） （ eISSN:1520-5126 ）

Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model. 査読

Inoue M, Ekimoto T, Yamane T, Ikeguchi M

Journal of chemical information and modeling   64 ( 9 )   3884 - 3895   2024年04月（ ISSN:1549-9596 ） （ eISSN:1549-960X ）

Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2. 査読

Park JH, Kawakami K, Ishimoto N, Ikuta T, Ohki M, Ekimoto T, Ikeguchi M, Lee DS, Lee YH, Tame JRH, Inoue A, Park SY

Nature communications   14 ( 1 )   7150 - 7150   2023年11月

Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study. 査読

Yamane T, Nakayama T, Ekimoto T, Inoue M, Ikezaki K, Sekiguchi H, Kuramochi M, Terao Y, Judai K, Saito M, Ikeguchi M, Sasaki YC

International journal of molecular sciences   24 ( 20 )   15423 - 15423   2023年10月（ eISSN:1422-0067 ）

Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding. 査読

Kurihara Y, Ekimoto T, Gordon CT, Uchijima Y, Sugiyama R, Kitazawa T, Iwase A, Kotani R, Asai R, Pingault V, Ikeguchi M, Amiel J, Kurihara H

The Journal of clinical investigation   133 ( 4 )   2023年02月（ ISSN:0021-9738 ）

TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction. 査読

Sakaniwa K, Fujimura A, Shibata T, Shigematsu H, Ekimoto T, Yamamoto M, Ikeguchi M, Miyake K, Ohto U, Shimizu T

Nature communications   14 ( 1 )   164   2023年01月（ eISSN:2041-1723 ）

Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease. 査読

Moritsugu K, Ekimoto T, Ikeguchi M, Kidera A

Journal of chemical information and modeling   63 ( 1 )   240 - 250   2023年01月（ ISSN:1549-9596 ）

Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA. 査読

Kidera A, Moritsugu K, Ekimoto T, Ikeguchi M

Biophysical reviews   14 ( 6 )   1473 - 1485   2022年12月（ ISSN:1867-2450 ）

Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D. 査読

Tanaka T, Ekimoto T, Nagatomo M, Neyazaki M, Shimoji E, Yamane T, Kanagawa S, Oi R, Mihara E, Takagi J, Akashi S, Ikeguchi M, Nogi T

Protein science : a publication of the Protein Society   31 ( 11 )   e4452   2022年11月（ ISSN:0961-8368 ）

3D-RISM-AI: A Machine Learning Approach to Predict Protein-Ligand Binding Affinity Using 3D-RISM. 査読

Osaki K, Ekimoto T, Yamane T, Ikeguchi M

The journal of physical chemistry. B   126 ( 33 )   6148 - 6158   2022年08月（ ISSN:1520-6106 ）

Structure of SARS-CoV-2 membrane protein essential for virus assembly. 査読

Zhang Z, Nomura N, Muramoto Y, Ekimoto T, Uemura T, Liu K, Yui M, Kono N, Aoki J, Ikeguchi M, Noda T, Iwata S, Ohto U, Shimizu T

Nature communications   13 ( 1 )   4399 - 4399   2022年08月

Correction to "Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane". 査読

Kohei Sato, Ryo Sasaki, Ryoto Matsuda, Mayuko Nakagawa, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi, Kazuhito V Tabata, Hiroyuki Noji, Kazushi Kinbara

Journal of the American Chemical Society   144 ( 30 )   13983 - 13984   2022年08月

Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane. 査読

Sato K, Sasaki R, Matsuda R, Nakagawa M, Ekimoto T, Yamane T, Ikeguchi M, Tabata KV, Noji H, Kinbara K

Journal of the American Chemical Society   144 ( 26 )   11802 - 11809   2022年06月（ ISSN:0002-7863 ）

Development of the force field for cyclosporine A. 査読

Yamane T, Ekimoto T, Ikeguchi M

Biophysics and physicobiology   19   e190045   2022年（ ISSN:2189-4779 ）

Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1. 査読

Kori S, Shibahashi Y, Ekimoto T, Nishiyama A, Yoshimi S, Yamaguchi K, Nagatoishi S, Ohta M, Tsumoto K, Nakanishi M, Defossez PA, Ikeguchi M, Arita K

Bioorganic & medicinal chemistry   52   116500 - 116500   2021年12月（ ISSN:0968-0896 ）

Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble. 査読

Kidera A, Moritsugu K, Ekimoto T, Ikeguchi M

Journal of molecular biology   433 ( 24 )   167324 - 167324   2021年12月（ ISSN:0022-2836 ）

Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Receptor. 査読

Takedomi K, Ohta M, Ekimoto T, Ikeguchi M

Journal of chemical information and modeling   61 ( 7 )   3583 - 3592   2021年07月（ ISSN:1549-9596 ）

Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations. 査読

Ekimoto T, Kudo T, Yamane T, Ikeguchi M

Journal of chemical information and modeling   61 ( 7 )   3625 - 3637   2021年07月（ ISSN:1549-9596 ）

Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion. 査読

Tamura-Sakaguchi R, Aruga R, Hirose M, Ekimoto T, Miyake T, Hizukuri Y, Oi R, Kaneko MK, Kato Y, Akiyama Y, Ikeguchi M, Iwasaki K, Nogi T

Acta crystallographica. Section D, Structural biology   77 ( Pt 5 )   645 - 662   2021年05月

Structural and dynamical insights into the PH domain of p62 in human TFIIH. 査読

Okuda M, Ekimoto T, Kurita JI, Ikeguchi M, Nishimura Y

Nucleic acids research   49 ( 5 )   2916 - 2930   2021年03月（ ISSN:0305-1048 ）

Front Cover: Imidazolinium‐based Multiblock Amphiphile as Transmembrane Anion Transporter (2/2021) 査読

Miki Mori, Kohei Sato, Toru Ekimoto, Shinichi Okumura, Mitsunori Ikeguchi, Kazuhito V. Tabata, Hiroyuki Noji, Kazushi Kinbara

Chemistry – An Asian Journal   16 ( 2 )   110 - 110   2021年01月

Imidazolinium-based Multiblock Amphiphile as Transmembrane Anion Transporter. 査読

Mori M, Sato K, Ekimoto T, Okumura S, Ikeguchi M, Tabata KV, Noji H, Kinbara K

Chemistry, an Asian journal   16 ( 2 )   147 - 157   2021年01月

Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain. 査読

Kori S, Jimenji T, Ekimoto T, Sato M, Kusano F, Oda T, Unoki M, Ikeguchi M, Arita K

Journal of molecular biology   432 ( 14 )   4061 - 4075   2020年06月（ ISSN:0022-2836 ）

A synthetic ion channel with anisotropic ligand response. 査読

Muraoka T, Noguchi D, Kasai RS, Sato K, Sasaki R, Tabata KV, Ekimoto T, Ikeguchi M, Kamagata K, Hoshino N, Noji H, Akutagawa T, Ichimura K, Kinbara K

Nature communications   11 ( 1 )   2924 - 2924   2020年06月

An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins. 査読

Hikiri S, Hayashi T, Inoue M, Ekimoto T, Ikeguchi M, Kinoshita M

The Journal of chemical physics   150 ( 17 )   175101 - 175101   2019年05月（ ISSN:0021-9606 ） （ eISSN:1089-7690 ）

Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments.

Ekimoto T, Kokabu Y, Oroguchi T, Ikeguchi M

Biophysics and physicobiology   16   377 - 390   2019年（ ISSN:2189-4779 ）

Rotational Mechanism Model of the Bacterial V(1) Motor Based on Structural and Computational Analyses. 査読

Singharoy A, Chipot C, Ekimoto T, Suzuki K, Ikeguchi M, Yamato I, Murata T

Frontiers in physiology   10   46 - 46   2019年（ ISSN:1664-042X ） （ eISSN:1664-042X ）

Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method. 査読

Ekimoto T, Yamane T, Ikeguchi M

Journal of chemical theory and computation   14 ( 12 )   6544 - 6559   2018年12月（ ISSN:1549-9618 ）

Multiscale molecular dynamics simulations of rotary motor proteins. 査読

Ekimoto T, Ikeguchi M

Biophysical reviews   10 ( 2 )   605 - 615   2018年04月（ ISSN:1867-2469 ）

Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle X-Ray Scattering Data. 査読

Ekimoto T, Ikeguchi M

Advances in experimental medicine and biology   1105   237 - 258   2018年（ ISSN:0065-2598 ）

SAXS-MD法によるビタミンD受容体リガンド結合ドメインの アポ型およびアンタゴニスト結合型構造の解析 査読

穴見 康昭, 清水 伸隆, 浴本 亨, 江川 大地, 伊藤 俊将, 池口 満徳, 山本 恵子

ビタミン   92 ( 1 )   18 - 20   2018年（ ISSN:0006-386X ） （ eISSN:2424-080X ）

Rotation Mechanism of Molecular Motor V(1)-ATPase Studied by Multiscale Molecular Dynamics Simulation. 査読

Isaka Y, Ekimoto T, Kokabu Y, Yamato I, Murata T, Ikeguchi M

Biophysical journal   112 ( 5 )   911 - 920   2017年03月（ ISSN:0006-3495 ） （ eISSN:1542-0086 ）

SAXS-MD解析を用いたビタミンD受容体のアポ型及びアンタゴニスト結合型構造の解析 査読

山本 恵子, 穴見 康昭, 清水 伸隆, 浴本 亨, 江川 大地, 伊藤 俊将, 池口 満徳

日本薬学会年会要旨集   137年会 ( 2 )   94 - 94   2017年03月（ ISSN:0918-9823 ）

Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics. 査読

Anami Y, Shimizu N, Ekimoto T, Egawa D, Itoh T, Ikeguchi M, Yamamoto K

Journal of medicinal chemistry   59 ( 17 )   7888 - 900   2016年09月（ ISSN:0022-2623 ） （ eISSN:1520-4804 ）

An accurate and efficient computation method of the hydration free energy of a large, complex molecule. 査読

Yoshidome T, Ekimoto T, Matubayasi N, Harano Y, Kinoshita M, Ikeguchi M

The Journal of chemical physics   142 ( 17 )   175101 - 175101   2015年05月（ ISSN:0021-9606 ） （ eISSN:1089-7690 ）

Finite-size effect on the charging free energy of protein in explicit solvent. 査読

Toru Ekimoto, Nobuyuki Matubayasi, Mitsunori Ikeguchi

Journal of chemical theory and computation   11 ( 1 )   215 - 23   2015年01月（ ISSN:1549-9618 ） （ eISSN:1549-9626 ）

Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by a Combination Andlysis of MD Simulations and SAXS Experiments

Yasuaki Anami, Nobutaka Shimizu, Toru Ekimoto, Daichi Egawa, Toshimasa Itoh, Mitsunori Ikeguchi, Keiko Yamamoto

BIOPHYSICAL JOURNAL   112 ( 3 )   48A - 48A   2017年02月（ ISSN:0006-3495 ） （ eISSN:1542-0086 ）

SAXS-MD解析を用いたビタミンD受容体のアポ型及びアンタゴニスト結合型構造の解析

山本恵子, 穴見康昭, 清水伸隆, 浴本亨, 江川大地, 伊藤俊将, 池口満徳

日本薬学会年会要旨集(CD-ROM)   137th   2017年

神経軸索ガイダンス分子セマフォリンと受容体の相互作用のin silico解析

下地恵令奈, 山根努, 浴本亨, 禾晃和, 池口満徳

日本蛋白質科学会年会プログラム・要旨集   17th   2017年

An Accurate and Efficient, Computational Method for the Hydration Free Energy of Large and Complex Molecules 査読

Takashi Yoshidome, Toru Ekimoto, Nobuyuki Matubayasi, Yuichi Harano, Masahiro Kinoshita, Mitsunori Ikeguchi

BIOPHYSICAL JOURNAL   110 ( 3 )   328A - 329A   2016年02月（ ISSN:0006-3495 ） （ eISSN:1542-0086 ）

神経軸索伸長ガイダンス分子セマフォリンと受容体プレキシンのタンパク質複合体の分子モデリング

下地恵令奈, 山根努, 浴本亨, 禾晃和, 池口満徳

日本蛋白質科学会年会プログラム・要旨集   16th   2016年

X線小角散乱(SAXS)と分子動力学計算(MD)を組み合わせたSAXS-MD法によるビタミンD受容体リガンド結合領域の相関構造解析

穴見康昭, 清水伸隆, 浴本亨, 江川大地, 伊藤俊将, 池口満徳, 山本恵子

日本薬学会関東支部大会講演要旨集   59th   2015年