Multi-scale molecular dynamics simulation on biomolecular dynamics in crowded cellular environments

• Project/Area Number: 19H05645
• Research Category: Grant-in-Aid for Scientific Research (S)
• Allocation Type: Single-year Grants
• Review Section: Broad Section G
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: 杉田 有治 国立研究開発法人理化学研究所, 開拓研究本部, 主任研究員 (80311190)
• Co-Investigator(Kenkyū-buntansha): 伊藤 隆 東京都立大学, 理学研究科, 教授 (80261147) ; 優 乙石 前橋工科大学, 工学部, 准教授 (90402544)
• Project Period (FY): 2019-06-26 – 2024-03-31
• Project Status: Completed (Fiscal Year 2023)
• Budget Amount: ¥198,120,000 (Direct Cost: ¥152,400,000、Indirect Cost: ¥45,720,000); Fiscal Year 2023: ¥32,630,000 (Direct Cost: ¥25,100,000、Indirect Cost: ¥7,530,000); Fiscal Year 2022: ¥40,430,000 (Direct Cost: ¥31,100,000、Indirect Cost: ¥9,330,000); Fiscal Year 2021: ¥33,800,000 (Direct Cost: ¥26,000,000、Indirect Cost: ¥7,800,000); Fiscal Year 2020: ¥62,270,000 (Direct Cost: ¥47,900,000、Indirect Cost: ¥14,370,000); Fiscal Year 2019: ¥28,990,000 (Direct Cost: ¥22,300,000、Indirect Cost: ¥6,690,000)
• Keywords: 分子動力学 / 分子混雑環境 / NMR / 酵素反応解析 / 機械学習 / マルチスケール / 細胞内環境 / 液液相分離 / 蛋白質構造柔軟性 / 酵素反応 / 蛋白質の構造柔軟性 / マルチスケールシミュレーション

Outline of Research at the Start

細胞内環境において安定な立体構造を持たない天然変性蛋白質や非特異的な相互作用による巨大な凝集体の形成などの新しい現象も発見されている。分子から細胞スケールに至る広い時空間で生じる生命現象を理解するために、粒子を粗視化したモデル、全原子モデル、活性部位のみを量子化学的に扱うQM/MMモデルを含むマルチスケール分子動力学法を開発し、異なるスケールのシミュレーションをベイズ推定に基づく理論で接続する。開発したシミュレーション法を用いて、細胞内環境における酵素反応、蛋白質の構造柔軟性と液液相分離の関係などを解明する。さらに、実験を用いて検証することで、分子モデルと計算手法の改良を行う。

Outline of Annual Research Achievements

マルチスケール分子動力学プログラムGENESISの開発を継続し、粗視化モデルを用いた大規模並列プログラムCGDYNを完成させた。このプログラムでは、陰溶媒モデルを用いた場合に発生する粒子密度の不均一性に起因する速度低下を防ぐために、シミュレーション空間を不均一に分割する新しいアルゴリズムを開発し、「富岳」などで他のソフトウェアを凌駕するパフォーマンスを得た。QM/MM計算を周期的境界条件で実現するための手法開発を行い、大規模な分子系の反応解析を行うことができるようになった。
応用研究対象の一つであるGRB2については，SOS1との相互作用によって形成される液滴のサイズと，GRB中のSH3ドメイン数およびSOS1中のPRM数との相関について解析を行った．また，メチル選択標識試料を用いた滴定実験より，LLPS形成時の相互作用に関わる可能性があるアミノ酸残基が示された．さらに，GRB2とSOS1由来のペプチドとのNMR滴定実験による精密な解離定数解析を行った．Drkについては，野生型の全長蛋白質，およびNSH3ドメインが安定化されたT22G変異体の全長蛋白質について解析を進め，野生型のNSH3ドメインの活性発現には他の因子の存在が必要であることを示唆する結果を得た．また、NMRとSAXSデータを組み合わせたIntegrative Modelingを行うことで、溶液中でのGRB2の動的構造を解析することに成功した。さらに、もう一つの応用研究対象であるトリプトファン合成酵素（TRPS）のインドール移動に伴う自由エネルギープロファイルを得ることができた。

Research Progress Status

令和5年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和5年度が最終年度であるため、記入しない。

Assessment Rating

Interim Assessment Comments (Rating)

A: In light of the aim of introducing the research area into the research categories, the expected progress has been made in research.

Research Products

• [Int'l Joint Research] University of Cambridge/University of Leicester(英国)
• [Int'l Joint Research] Goethe University Frankfurt(ドイツ)
• [Int'l Joint Research] ETH Zurich(スイス)
• [Int'l Joint Research] Michigan State University(米国)
• [Int'l Joint Research] Michigan State University(米国)
• [Int'l Joint Research] University of Cambridge/University of Leicester(英国)
• [Int'l Joint Research] Goethe University Frankfurt(ドイツ)
• [Int'l Joint Research] ETH Zurich(スイス)
• [Int'l Joint Research] Michigan State University(米国)
• [Int'l Joint Research] University of Cambridge/University of Leicester(英国)
• [Int'l Joint Research] Goethe University Frankfurt(ドイツ)
• [Int'l Joint Research] ETH Zurich(スイス)
• [Int'l Joint Research] Michigan State University/Leihigh University(米国)
• [Int'l Joint Research] University of Warsaw(ポーランド)
• [Int'l Joint Research] University of Cambridge/University of Leicester(英国)
• [Int'l Joint Research] Goethe University Frankfurt(ドイツ)
• [Int'l Joint Research] ETH Zurich(スイス)
• [Int'l Joint Research] Michigan State University/Lehigh University(米国)
• [Int'l Joint Research] University of Cambridge/University of Leicester(英国)
• [Int'l Joint Research] University of Warsaw(ポーランド)
• [Int'l Joint Research] Goethe University Frankfurt(ドイツ)
• [Int'l Joint Research] ETH Zurich(スイス)
• [Journal Article] SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations (2024)
  • Author(s): Isseki Yu, Takaharu Mori, Daisuke Matsuoka, Donatas Surblys, Yuji Sugita1
  • Journal Title: Journal of Computational Chemistry Volume: 45 Issue: 8 Pages: 498-505
  • DOI: 10.1002/jcc.27260
  • Peer Reviewed / Open Access
• [Journal Article] Free-energy landscapes of transmembrane homodimers by bias-exchange adaptively biased molecular dynamics (2024)
  • Author(s): Ito Shingo、Sugita Yuji
  • Journal Title: Biophysical Chemistry Volume: 307 Pages: 107190-107190
  • DOI: 10.1016/j.bpc.2024.107190
  • Peer Reviewed / Open Access
• [Journal Article] GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems (2024)
  • Author(s): Jung Jaewoon、Tan Cheng、Sugita Yuji
  • Journal Title: Nature Communications Volume: 15 Issue: 1 Pages: 3370-3370
  • DOI: 10.1038/s41467-024-47654-1
  • Peer Reviewed / Open Access
• [Journal Article] Direct Observation of Membrane-Associated H-Ras in the Native Cellular Environment by In-Cell ¹⁹F-NMR Spectroscopy (2023)
  • Author(s): Ikari Masaomi、Yagi Hiromasa、Kasai Takuma、Inomata Kohsuke、Ito Masahiro、Higuchi Kae、Matsuda Natsuko、Ito Yutaka、Kigawa Takanori
  • Journal Title: JACS Au Volume: 3 Issue: 6 Pages: 1658-1669
  • DOI: 10.1021/jacsau.3c00108
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural insights into the complex of oncogenic KRas4BG12V and Rgl2, a RalA/B activator (2023)
  • Author(s): M. Tariq, T. Ikeya, N. Togashi, L. Fairall, S. Kamei, S. Mayooramurugan, L.R. Abbott, A. Hasan, C. Bueno-Alejo, S. Sukegawa, B. Romartinez-Alonso, M.A.M. Campillo, A.J. Hudson, Y. Ito, J.W.R. Schwabe, C. Dominguez, K. Tanaka
  • Journal Title: Life Sci. Alliance Volume: 7 Issue: 1 Pages: e202302080-e202302080
  • DOI: 10.26508/lsa.202302080
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Interactions of the N- and C-Terminal SH3 Domains of Drosophila Drk with the Proline-Rich Peptides from Sos and Dos (2023)
  • Author(s): P.M. Sayeesh, M. Iguchi, Y. Suemoto, J. Inoue, K. Inomata, T. Ikeya, Y. Ito
  • Journal Title: Int. J. Mol. Sci. Volume: 24 Issue: 18 Pages: 14135-14135
  • DOI: 10.3390/ijms241814135
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer (2023)
  • Author(s): Jung Jaewoon、Kobayashi Chigusa、Sugita Yuji
  • Journal Title: Journal of Computational Chemistry Volume: - Issue: 20 Pages: 1740-1749
  • DOI: 10.1002/jcc.27124
  • Peer Reviewed
• [Journal Article] Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers (2023)
  • Author(s): Ugarte La Torre Diego、Takada Shoji、Sugita Yuji
  • Journal Title: The Journal of Chemical Physics Volume: 159 Issue: 7 Pages: 75101-75101
  • DOI: 10.1063/5.0160417
  • Peer Reviewed / Open Access
• [Journal Article] Development of Hidden Markov Modeling of Molecular Orientations and Structures from High-Speed Atomic Force Microscopy Time-Series Images (2023)
  • Author(s): Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
  • Journal Title: PLoS Comp. Biol. Volume: 18 Issue: 12 Pages: e1010384-e1010384
  • DOI: 10.1371/journal.pcbi.1010384
  • Peer Reviewed / Open Access
• [Journal Article] Highly charged proteins and their repulsive interactions antagonize biomolecular condensation (2023)
  • Author(s): Cheng Tan, Ai Niitsu, Yuji Sugita
  • Journal Title: JACS Au Volume: 3 Issue: 3 Pages: 834-848
  • DOI: 10.1021/jacsau.2c00646
  • Peer Reviewed / Open Access
• [Journal Article] Allosteric regulation of ホイ-reaction stage I in tryptophan synthase upon the ホア-ligand binding (2023)
  • Author(s): Shingo Ito, Kiyoshi Yagi, Yuji Sugita
  • Journal Title: J. Chem. Phys. Volume: 158 Issue: 11 Pages: 115101-115101
  • DOI: 10.1063/5.0134117
  • Peer Reviewed / Open Access
• [Journal Article] Structural Effects of Spike Protein D614G Mutation in SARS-CoV-2 (2022)
  • Author(s): Hisham M. Dokainish, Yuji Sugita
  • Journal Title: Biophys. J. Volume: 122 Issue: 14 Pages: 1-11
  • DOI: 10.1016/j.bpj.2022.11.025
  • Peer Reviewed / Open Access
• [Journal Article] Protein assembly and crowding simulations (2022)
  • Author(s): Lim Heo, Yuji Sugita, Michael Feig
  • Journal Title: Curr. Opin. Struct. Biol. Volume: 73 Pages: 102340-102340
  • DOI: 10.1016/j.sbi.2022.102340
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Implementation of residue-level coarse-grained models I GENESIS for large-scale molecular dynamics simulations (2022)
  • Author(s): Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte, Shoji Takada, Yuji Sugita
  • Journal Title: PLoS Comp. Biol. Volume: 18 Issue: 4 Pages: e1009578-e1009578
  • DOI: 10.1371/journal.pcbi.1009578
  • Peer Reviewed / Open Access
• [Journal Article] Computational analysis on the allostery of tryptophan synthase: relationship between α/β-ligand binding and distal domain closure (2022)
  • Author(s): Shingo Ito, Kiyoshi Yagi, Yuji Sugita
  • Journal Title: J. Phys. Chem. B Volume: 126 Issue: 17 Pages: 3300-3308
  • DOI: 10.1021/acs.jpcb.2c01556
  • Peer Reviewed / Open Access
• [Journal Article] Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics (2022)
  • Author(s): Shinobu Ai、Re Suyong、Sugita Yuji
  • Journal Title: Frontiers in Molecular Biosciences Volume: 9 Pages: 878830-878830
  • DOI: 10.3389/fmolb.2022.878830
  • Peer Reviewed / Open Access
• [Journal Article] Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions (2022)
  • Author(s): Hiraku Oshima, Yuji Sugita
  • Journal Title: J. Chem. Inf. Model. Volume: 62 Issue: 11 Pages: 2846-2856
  • DOI: 10.1021/acs.jcim.1c01532
  • Peer Reviewed / Open Access
• [Journal Article] Protein Folding Intermediates on the Dimensionality Reduced Landscape with UMAP and Native Contact Likelihood (2022)
  • Author(s): Mao Oide, Yuji Sugita
  • Journal Title: J. Chem. Phys. Volume: 157 Issue: 7 Pages: 75101-75101
  • DOI: 10.1063/5.0099094
  • Peer Reviewed / Open Access
• [Journal Article] Modified protein-water interactions in CHARMM36m for thermodynamics and kinetics of proteins in dilute and crowded solutions (2022)
  • Author(s): Daiki Matsubara, Kento Kasahara, Hisham Dokainish, Hiraku Oshima, Yuji Sugita
  • Journal Title: Molecules Volume: 27 Issue: 17 Pages: 5726-5726
  • DOI: 10.3390/molecules27175726
  • Peer Reviewed / Open Access
• [Journal Article] Yuxia Zhang, Chigusa Kobayashi, Xiaohan Cai, Satoshi Watanabe, Akihisa Tsutsumi, Masahide Kikkawa, Yuji Sugita, Kenji Inaba (2022)
  • Author(s): Yuxia Zhang, Chigusa Kobayashi, Xiaohan Cai, Satoshi Watanabe, Akihisa Tsutsumi, Masahide Kikkawa, Yuji Sugita, Kenji Inaba
  • Journal Title: Cell reports Volume: 41 Issue: 10 Pages: 111760-111760
  • DOI: 10.1016/j.celrep.2022.111760
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation (2022)
  • Author(s): Matsunaga Yasuhiro、Kamiya Motoshi、Oshima Hiraku、Jung Jaewoon、Ito Shingo、Sugita Yuji
  • Journal Title: Biophysical Reviews Volume: 14 Issue: 6 Pages: 1503-1512
  • DOI: 10.1007/s12551-022-01030-9
  • Peer Reviewed / Open Access
• [Journal Article] Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation (2022)
  • Author(s): Ai Niitsu, Yuji Sugita
  • Journal Title: Biophys. Rev. Volume: 14 Issue: 5 Pages: 1-10
  • DOI: 10.1039/d2cp03972a
  • Peer Reviewed / Open Access
• [Journal Article] Insight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos (2022)
  • Author(s): Sayeesh P.M., Ikeya, T., Sugasawa, H., Watanabe, R., Mishima, M., Inomata, K., & Ito, Y.
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 625 Pages: 87-93
  • DOI: 10.1016/j.bbrc.2022.08.007
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Weight average approaches for predicting dynamical properties of biomolecules (2022)
  • Author(s): Yagi Kiyoshi、Re Suyong、Mori Takaharu、Sugita Yuji
  • Journal Title: Current Opinion in Structural Biology Volume: 72 Pages: 88-94
  • DOI: 10.1016/j.sbi.2021.08.008
  • Peer Reviewed
• [Journal Article] The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein (2022)
  • Author(s): Dokainish Hisham M、Re Suyong、Mori Takaharu、Kobayashi Chigusa、Jung Jaewoon、Sugita Yuji
  • Journal Title: eLife Volume: 11
  • DOI: 10.7554/elife.75720
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural Biology Studies to Understand the Mechanism of SARS-CoV-2 Infection (2021)
  • Author(s): 伊藤 隆
  • Journal Title: Earozoru Kenkyu Volume: 36 Issue: 4 Pages: 237-245
  • DOI: 10.11203/jar.36.237
  • NAID: 130008132519
  • ISSN: 0912-2834, 1881-543X
  • Year and Date: 2021-12-20
  • Peer Reviewed / Open Access
• [Journal Article] Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations (2021)
  • Author(s): Yagi Kiyoshi、Ito Shingo、Sugita Yuji
  • Journal Title: The Journal of Physical Chemistry B Volume: 125 Issue: 18 Pages: 4701-4713
  • DOI: 10.1021/acs.jpcb.1c01862
  • Peer Reviewed
• [Journal Article] Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins (2021)
  • Author(s): A. Shinobu, C. Kobayashi, Y. Matsunaga, and Y. Sugita
  • Journal Title: Journal of Chemical Information and Modeling Volume: 61 Issue: 5 Pages: 2427-2443
  • DOI: 10.1021/acs.jcim.1c00286
  • Peer Reviewed / Open Access
• [Journal Article] Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps (2021)
  • Author(s): Mori Takaharu、Terashi Genki、Matsuoka Daisuke、Kihara Daisuke、Sugita Yuji
  • Journal Title: Journal of Chemical Information and Modeling Volume: 61 Issue: 7 Pages: 3516-3528
  • DOI: 10.1021/acs.jcim.1c00230
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Reduced Efficacy of a Src Kinase Inhibitor in Crowded Protein Solution. (2021)
  • Author(s): Kento Kasahara, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Miyata-Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, Yuji Sugita
  • Journal Title: Nature Communications Volume: 12 Issue: 1 Pages: 4099-4099
  • DOI: 10.1038/s41467-021-24349-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems (2021)
  • Author(s): Jaewoon Jung, Kento Kasahara, Chigusa Kobayashi, Hiraku Oshima, Takaharu Mori, and Yuji Sugita
  • Journal Title: J. Chem. Theory Comput. Volume: 17 Issue: 8 Pages: 5312-5321
  • DOI: 10.1021/acs.jctc.1c00185
  • Peer Reviewed / Open Access
• [Journal Article] Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin (2021)
  • Author(s): Yagi Kiyoshi、Sugita Yuji
  • Journal Title: Journal of Chemical Theory and Computation Volume: 17 Issue: 8 Pages: 5007-5020
  • DOI: 10.1021/acs.jctc.1c00060
  • Peer Reviewed
• [Journal Article] Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons (2021)
  • Author(s): Fujiyama Keisuke、Kato Naoki、Re Suyong、Kinugasa Kiyomi、Watanabe Kohei、Takita Ryo、Nogawa Toshihiko、Hino Tomoya、Osada Hiroyuki、Sugita Yuji、Takahashi Shunji、Nagano Shingo
  • Journal Title: Angewandte Chemie International Edition Volume: 60 Issue: 41 Pages: 22401-22410
  • DOI: 10.1002/anie.202106186
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase (2021)
  • Author(s): C. Kobayashi, Y. Matsunaga, J. Jung, Y. Sugita
  • Journal Title: Proceeding of the National Academy of Sciences of the United States of America Volume: 118 Issue: 40
  • DOI: 10.1073/pnas.2105507118
  • Peer Reviewed / Open Access
• [Journal Article] Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE (2021)
  • Author(s): Takayuki Nagae, Masashi Unno, Taiki Koizumi, Yohei Miyanoiri, Tomotsumi Fujisawa, Kento Masui, Takanari Kamo, Kei Wada, Toshihiko Eki, Yutaka Ito, Yuu Hirose, Masaki Mishima
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 118(20) Issue: 20
  • DOI: 10.1073/pnas.2024583118
  • Peer Reviewed / Open Access
• [Journal Article] Molecular mechanism of glycolytic flux control intrinsic to human phosphoglycerate kinase (2021)
  • Author(s): Hiromasa Yagi, Takuma Kasai, Elisa Rioual, Teppei Ikeya, Takanori Kigawa
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America Volume: 118 Issue: 50
  • DOI: 10.1073/pnas.2112986118
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 溶液NMR法を用いた蛋白質立体構造計算の最近の動向 (2021)
  • Author(s): 池谷鉄兵，伊藤 隆
  • Journal Title: 細胞 Volume: 53 Pages: 48-52
  • NAID: 40022675452
  • Peer Reviewed
• [Journal Article] 溶液NMR法を用いた蛋白質立体構造計算の最近の動向 (2021)
  • Author(s): 池谷鉄兵，伊藤 隆
  • Journal Title: アグリバイオ Volume: 5 Pages: 980-986
  • NAID: 40022675452
  • Peer Reviewed
• [Journal Article] Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations (2021)
  • Author(s): Ren Weitong、Dokainish Hisham M.、Shinobu Ai、Oshima Hiraku、Sugita Yuji
  • Journal Title: The Journal of Physical Chemistry B Volume: 125 Issue: 11 Pages: 2898-2909
  • DOI: 10.1021/acs.jpcb.0c11600
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein (2021)
  • Author(s): Mori Takaharu、Jung Jaewoon、Kobayashi Chigusa、Dokainish Hisham M.、Re Suyong、Sugita Yuji
  • Journal Title: Biophysical Journal Volume: 120 Issue: 6 Pages: 1060-1071
  • DOI: 10.1016/j.bpj.2021.01.012
  • Peer Reviewed / Open Access
• [Journal Article] Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution (2021)
  • Author(s): Kulik Marta、Mori Takaharu、Sugita Yuji
  • Journal Title: Frontiers in Molecular Biosciences Volume: 8
  • DOI: 10.3389/fmolb.2021.631854
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems (2020)
  • Author(s): Jung Jaewoon、Kobayashi Chigusa、Kasahara Kento、Tan Cheng、Kuroda Akiyoshi、Minami Kazuo、Ishiduki Shigeru、Nishiki Tatsuo、Inoue Hikaru、Ishikawa Yutaka、Feig Michael、Sugita Yuji
  • Journal Title: Journal of Computational Chemistry Volume: 42 Issue: 4 Pages: 231-241
  • DOI: 10.1002/jcc.26450
  • Peer Reviewed
• [Journal Article] Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling (2020)
  • Author(s): Dokainish Hisham M.、Sugita Yuji
  • Journal Title: International Journal of Molecular Sciences Volume: 22 Issue: 1 Pages: 270-270
  • DOI: 10.3390/ijms22010270
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step (2020)
  • Author(s): Jung Jaewoon、Sugita Yuji
  • Journal Title: The Journal of Chemical Physics Volume: 153 Issue: 23 Pages: 234115-234115
  • DOI: 10.1063/5.0027873
  • Peer Reviewed
• [Journal Article] CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations (2020)
  • Author(s): Kim Seonghoon、Oshima Hiraku、Zhang Han、Kern Nathan R.、Re Suyong、Lee Jumin、Roux Benoit、Sugita Yuji、Jiang Wei、Im Wonpil
  • Journal Title: Journal of Chemical Theory and Computation Volume: 16 Issue: 11 Pages: 7207-7218
  • DOI: 10.1021/acs.jctc.0c00884
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion (2020)
  • Author(s): Matoba Kazuaki、Kotani Tetsuya、Tsutsumi Akihisa、Tsuji Takuma、Mori Takaharu、Noshiro Daisuke、Sugita Yuji、Nomura Norimichi、Iwata So、Ohsumi Yoshinori、Fujimoto Toyoshi、Nakatogawa Hitoshi、Kikkawa Masahide、Noda Nobuo N.
  • Journal Title: Nature Structural & Molecular Biology Volume: 27 Issue: 12 Pages: 1185-1193
  • DOI: 10.1038/s41594-020-00518-w
  • Peer Reviewed / Open Access
• [Journal Article] Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method (2020)
  • Author(s): Oshima Hiraku、Re Suyong、Sugita Yuji
  • Journal Title: Journal of Chemical Information and Modeling Volume: 60 Issue: 11 Pages: 5382-5394
  • DOI: 10.1021/acs.jcim.0c00338
  • Peer Reviewed
• [Journal Article] A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations (2020)
  • Author(s): Tan Cheng、Jung Jaewoon、Kobayashi Chigusa、Sugita Yuji
  • Journal Title: The Journal of Chemical Physics Volume: 153 Issue: 4 Pages: 044110-044110
  • DOI: 10.1063/5.0013089
  • Peer Reviewed
• [Journal Article] In-cell NMR as a sensitive tool to monitor physiological condition of Escherichia coli (2020)
  • Author(s): Sugiki Toshihiko、Yamaguchi Yoshihiro、Fujiwara Toshimichi、Inouye Masayori、Ito Yutaka、Kojima Chojiro
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 2466-2466
  • DOI: 10.1038/s41598-020-59076-2
  • NAID: 120006952208
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] In situ structural biology using in-cell NMR (2020)
  • Author(s): Nishida Noritaka、Ito Yutaka、Shimada Ichio
  • Journal Title: Biochimica et Biophysica Acta (BBA) - General Subjects Volume: 1864 Issue: 2 Pages: 129364-129364
  • DOI: 10.1016/j.bbagen.2019.05.007
  • Peer Reviewed
• [Journal Article] Domain selective labeling for NMR studies of multidomain proteins by domain ligation using highly active sortase A (2020)
  • Author(s): Aizu Takahiro、Suzuki Takumi、Kido Akihiro、Nagai Kan、Kobayashi Ayaho、Sugiura Reiko、Ito Yutaka、Mishima Masaki
  • Journal Title: Biochimica et Biophysica Acta (BBA) - General Subjects Volume: 1864 Issue: 2 Pages: 129419-129419
  • DOI: 10.1016/j.bbagen.2019.129419
  • Peer Reviewed
• [Journal Article] Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T (2020)
  • Author(s): Tamura Koichi、Sugita Yuji
  • Journal Title: The Journal of Physical Chemistry Letters Volume: 11 Issue: 8 Pages: 2824-2829
  • DOI: 10.1021/acs.jpclett.0c00547
  • Peer Reviewed
• [Journal Article] Use of single-molecule time-series data for refining conformational dynamics in molecular simulations (2020)
  • Author(s): Matsunaga Yasuhiro、Sugita Yuji
  • Journal Title: Current Opinion in Structural Biology Volume: 61 Pages: 153-159
  • DOI: 10.1016/j.sbi.2019.12.022
  • Peer Reviewed / Open Access
• [Presentation] NMR studies of multi-domain adaptor proteins in signal transduction pathways (2024)
  • Author(s): Yutaka Ito，Teppei Ikeya，Sayeesh P.M.，Mao Oide，Yuji Sugita
  • Organizer: TJ2024 (Taiwan-Japan NMR Symposium 2024)
  • Int'l Joint Research / Invited
• [Presentation] In-cell NMRを用いたKeap1-Nrf2系の解析 (2024)
  • Author(s): 伊藤 隆
  • Organizer: NMRシンポジウム―環境応答の構造生物学
  • Invited
• [Presentation] Protein Functions in Crowded Cellular Environments (2024)
  • Author(s): Yuji Sugita
  • Organizer: The 6th Symposium on Biophysics Postgraduate Research in Hong Kong
  • Int'l Joint Research / Invited
• [Presentation] Integrated Modeling of Flexible Multi-Domain Protein Structures in Solution (2024)
  • Author(s): Yuji Sugita, Mao Oide, Teppei Ikeya, Yutaka Ito
  • Organizer: 9th Polish-Korean Conference on Protein Folding
  • Int'l Joint Research / Invited
• [Presentation] Refinement of Markov State Model using experimental data and nonlinear dimensional reduction methods (2024)
  • Author(s): Yuji Sugita
  • Organizer: ACS Symposium on Markov State Modeling of Conformational Dynamics in the Wake of Machine Learning
  • Int'l Joint Research / Invited
• [Presentation] Molecular dynamics simulation of the substrate channeling in tryptophan synthetase (2023)
  • Author(s): 優乙石, 伊東真吾, 八木清, 杉田有治
  • Organizer: 第61回生物物理学会年会
• [Presentation] In-cell NMR studies of the Keap1-Nrf2 system (2023)
  • Author(s): Yutaka Ito，Mei Toyoda，Shiori Suehiro，Kaito Shima，Teppei Ikeya，Takafumi Suzuki, Masayuki Yamamoto, Kohsuke Inomata
  • Organizer: Asia-Pacific Nuclear Magnetic Resonance (APNMR) 2023
  • Int'l Joint Research / Invited
• [Presentation] 多次元NMRの原理 (2023)
  • Author(s): 伊藤 隆
  • Organizer: 2023年度日本分光学会主催秋期セミナー「NMR分光法の基礎と応用」
  • Invited
• [Presentation] Analysis of the mechanism underlying multivalent interactions between GRB2 and SOS1 and their LLPS using solution NMR (2023)
  • Author(s): Teppei Ikeya，Mao Oide，W. Ren，Keita Tateno，Takami Ando，Haruka Sugasawa，Yuji Sugita，Yutaka Ito
  • Organizer: 第61回生物物理学会年会
• [Presentation] GRB2とSOS1による多価相互作用と液液相分離の溶液NMR解析 (2023)
  • Author(s): 池谷鉄兵，菅澤はるか，富樫直之，林 俊文，美川 務，杉田有治，伊藤 隆
  • Organizer: 第62回NMR討論会
• [Presentation] In-cell NMRにおける細胞試料管理 (2023)
  • Author(s): 猪股晃介，豊田芽生，島 海翔，長峰萌華，末広志織，池谷鉄兵，鈴木隆史，山本雅之，伊藤 隆
  • Organizer: 第62回NMR討論会
• [Presentation] Interaction of N-and C-terminal SH3 domains of Drosophila adapter protein Drk with Sos and Dos (2023)
  • Author(s): Sayeesh PM，Mayuki Iguchi，Haruka Sugasawa，Kahsuke Inomata，Teppei Ikeya，Yutaka Ito
  • Organizer: The 19th European Magnetic Resonance Congress
  • Int'l Joint Research
• [Presentation] In-cell NMRを用いたlinear diubiquitinの細胞内での立体構造解析 (2023)
  • Author(s): 屋部祥大，田岸亮馬，鴨志田一，美川 務，猪股晃介，池谷鉄兵，伊藤 隆
  • Organizer: 第62回NMR討論会
• [Presentation] 異種核多次元NMRによる根粒菌マルチドメイン蛋白質FixJの立体構造解析 (2023)
  • Author(s): 大久保里佳，堀川皓央，伊藤かおり，菱倉直樹，渡邉吏輝，三島正規，猪股晃介，小手石泰康，澤井仁美，城 宣嗣，池谷鉄兵，伊藤 隆
  • Organizer: 第62回NMR討論会
• [Presentation] Structural and dynamic studies on the Drosophila adapter Protein Drk (2023)
  • Author(s): Sayeesh PM，Mayumi Iguchi，Teppei Ikeya，Yutaka Ito
  • Organizer: 第62回NMR討論会
• [Presentation] ストレス応答型の転写制御に関与するKeap1-Nrf2複合体のIn-cell NMR解析 (2023)
  • Author(s): 豊田芽生，猪股晃介，末広志織，島 海翔，長峰萌華，池谷鉄兵，鈴木隆史，山本雅之，伊藤 隆
  • Organizer: 第62回NMR討論会
• [Presentation] 溶液NMRによるKRASとRGL2の相互作用の解析 (2023)
  • Author(s): 助川咲良，富樫直之，P.M. Sayeesh，菅澤はるか，猪股晃介，田仲加代子，伊藤 隆，池谷鉄兵
  • Organizer: 第62回NMR討論会
• [Presentation] NMRピークの線形解析を用いたKRAS/RGL2RBD滴定データの定量化 (2023)
  • Author(s): 富樫直之，助川咲良，菅澤はるか，美川 務，猪股晃介，田仲加代子，伊藤 隆，池谷鉄兵
  • Organizer: 第62回NMR討論会
• [Presentation] Drk蛋白質のN末端およびC末端SH3ドメインとSos/Dos由来ペプチドとの相互作用解析 (2023)
  • Author(s): 井口真由美，P.M. Sayeesh，池谷鉄兵，伊藤 隆
  • Organizer: 第62回NMR討論会
• [Presentation] 溶液NMRによるUbiquitin C-terminal Hydrolase L3 (UCHL3)の構造・ダイナミクス解析 (2023)
  • Author(s): 宮田裕貴，菅澤はるか，猪股晃介，伊藤 隆，池谷鉄兵
  • Organizer: 第62回NMR討論会
• [Presentation] GRB2とSOS1による多価相互作用の溶液NMR解析 (2023)
  • Author(s): 林 俊文，館野桂太，菅澤はるか，池谷鉄兵，伊藤 隆
  • Organizer: 第62回NMR討論会
• [Presentation] 蛋白質の立体構造に対する分子クラウディングの影響の解析 (2023)
  • Author(s): 加藤聖人，Sayeesh PM，池谷鉄兵，伊藤 隆
  • Organizer: 第62回NMR討論会
• [Presentation] NMRによるFixL-FixJ二成分シグナル伝達系の機能解析 (2023)
  • Author(s): 菱倉直樹，渡邉吏輝，大久保里佳，堀川皓央，伊藤かおり，三島正規，猪股晃介，小手石泰康，澤井仁美，城 宣嗣，池谷鉄兵，伊藤 隆
  • Organizer: 第62回NMR討論会
• [Presentation] How cellular environments are regulated by non-specific molecular interaction (2023)
  • Author(s): Yuji Sugita
  • Organizer: Biomolecules and Nanostructures 8
  • Int'l Joint Research / Invited
• [Presentation] Multi-scale molecular dynamics simulations on protein function in intracellular environments (2023)
  • Author(s): Yuji Sugita
  • Organizer: CCP2023
  • Int'l Joint Research / Invited
• [Presentation] Accurate Langevin integration for isothermal-isobaric condition with a large time step (2023)
  • Author(s): Jaewoon Jung, Yuji Sugita
  • Organizer: CCP2023
  • Int'l Joint Research / Invited
• [Presentation] Enhanced Conformational Sampling for Protein Dynamics and Function (2023)
  • Author(s): Yuji Sugita
  • Organizer: 8th Polish-Korean Conference on Protein Folding
  • Int'l Joint Research / Invited
• [Presentation] Protein dynamics and functions using enhanced MD simulations (2023)
  • Author(s): Yuji Sugita
  • Organizer: CECAM Workshop
  • Int'l Joint Research / Invited
• [Presentation] Crowding effects on protein structure, dynamics, and functions (2023)
  • Author(s): Yuji Sugita
  • Organizer: The 21st KIAS Conference on Protein Folding and Function
  • Int'l Joint Research / Invited
• [Presentation] Regulation of Biomolecular Condensation Studied with Large-Scale Coarse-Grained Molecular Dynamics Simulations in GENESIS (2023)
  • Author(s): Cheng Tan, Ai Niitsu, Jaewoon Jung, Yuji Sugita
  • Organizer: 第61回生物物理学会年会
  • Invited
• [Presentation] Coarse-grained modeling and simulations of protein and lipid dynamics (2023)
  • Author(s): Yuji Sugita
  • Organizer: MBSJ
  • Invited
• [Presentation] Monomeric Structures of GRB2 in Solution by Integrated Modeling (2023)
  • Author(s): Yuji Sugita, Mao Oide, Teppei Ikeya, Yutaka Ito
  • Organizer: EMBO workshop on Computational Structural Biology
  • Int'l Joint Research / Invited
• [Presentation] Secondary structure and phase behavior of Hero proteins and their function in regulating biomolecular condensatio (2023)
  • Author(s): Cheng Tan
  • Organizer: 2nd BIE workshop
• [Presentation] Protein Dynamics and Functions using enhanced MD simulations (2023)
  • Author(s): Yuji Sugita
  • Organizer: The 23rd Sanibel Meeting
  • Int'l Joint Research / Invited
• [Presentation] Binding free energy landscape of c-Src kinase to its inhibitors sampled by molecular dynamics simulations: effect of ligand size and flexibility (2023)
  • Author(s): Ai Shinobu, Suyong Re, Yuji Sugita
  • Organizer: BPS2023
  • Int'l Joint Research
• [Presentation] 非断熱QM/MM分子動力学計算による光駆動タンパク質の反応ダイナミクス (2022)
  • Author(s): 八木清
  • Organizer: 第20回「高速分子動画」オンラインセミナー
  • Invited
• [Presentation] 量子化学と分子動力学の融合によるアニオン交換膜の理論解析 (2022)
  • Author(s): 八木清
  • Organizer: 第1回有機イオニクスワークショップ
  • Invited
• [Presentation] Reaction dynamics of light-driven protein studied by non-adiabatic QM/MM molecular dynamics simulations (2022)
  • Author(s): Kiyoshi Yagi
  • Organizer: Molecular Movies International Symposium 2022
  • Int'l Joint Research
• [Presentation] Conformational Dynamics and Functions of Proteins in Crowded Cellular Environments (2022)
  • Author(s): Yuji Sugita
  • Organizer: BPS Thematic Meeting Hamburg
  • Int'l Joint Research / Invited
• [Presentation] 細胞内環境における蛋白質の構造・ダイナミクス・機能 (2022)
  • Author(s): 杉田有治
  • Organizer: 第22回日本蛋白質科学会年会
  • Invited
• [Presentation] 分子動力学計算と実験データに基づくタンパク質複合体立体構造モデリング (2022)
  • Author(s): 森貴治
  • Organizer: 第22回日本蛋白質科学会年会
  • Invited
• [Presentation] 分子動力学計算によるトリプトファン合成酵素におけるアロステリック機構の解明 (2022)
  • Author(s): 伊東真吾,八木清,杉田有治
  • Organizer: 第22回日本蛋白質科学会年会
• [Presentation] 分子動力学計算によるF1-ATPaseのリン酸放出経路の探索 (2022)
  • Author(s): 本橋昌大, 大出真央, 宗行英朗, 杉田有治
  • Organizer: 第22回日本蛋白質科学会年会
• [Presentation] クライオ電子顕微鏡像に基づく蛋白質動態の自由エネルギー地形推定法の開発と検討 (2022)
  • Author(s): 大出真央, 杉田有治
  • Organizer: 第22回日本蛋白質科学会年会
• [Presentation] Src Kinase inhibitor binding free energy landscape sampled by Molecular-dynamics simulations: effect of ligand size and flexibility (2022)
  • Author(s): 信夫愛、李秀栄、杉田有治
  • Organizer: 第22回日本蛋白質科学会年会
• [Presentation] 静電相互作用計算を高速化した自由エネルギー摂動法の開発 (2022)
  • Author(s): 尾嶋拓, 杉田有治
  • Organizer: 第22回日本蛋白質科学会年会
• [Presentation] 計算科学で挑む細胞内環境の生物学 (2022)
  • Author(s): 杉田有治
  • Organizer: 第48回生体分子科学討論会
  • Invited
• [Presentation] Free-energy calculations of protein-ligand binding in solution and crowded environments (2022)
  • Author(s): Yuji Sugita
  • Organizer: WCB2022
  • Int'l Joint Research / Invited
• [Presentation] QM/MM法の開発と生体分子の振動解析と化学反応への応用 (2022)
  • Author(s): 八木清
  • Organizer: 物性研短期研究会「理論タンパク質物性科学の最前線：理論と実験との密な協働」
  • Invited
• [Presentation] 分子動力学ソフトウェアGENESISの開発と細胞内における蛋白質動態解析 (2022)
  • Author(s): 杉田有治
  • Organizer: 兵庫県MI研究会
  • Invited
• [Presentation] De novo design of membrane coiled-coil barrels (2022)
  • Author(s): Ai Niitsu, Andrew R Thomson, Alistair Scott, Jason T Sengel, Kozhinjampara R Mahendran, Yuji Sugita, R Leo Brady, Mark I Wallace, Hagan Bayley, and Derek N Woolfson
  • Organizer: Alpbach Workshop: Coiled coils, fibrous & repeat proteins
  • Int'l Joint Research / Invited
• [Presentation] Stability and dynamics of de novo designed transmembrane peptide barrels (2022)
  • Author(s): Ai Niitsu, Jaewoon Jung, and Yuji Sugita
  • Organizer: 第60回日本生物物理学会年会
  • Invited
• [Presentation] Development of the free-energy perturbation method toward drug discovery on supercomputer Fugaku (2022)
  • Author(s): 尾嶋拓, 杉田有治
  • Organizer: 第60回日本生物物理学会年会
  • Invited
• [Presentation] Binding free energy landscapes of Src Kinase to its inhibitors sampled by two-dimensional replica exchange molecular dynamics simulations (2022)
  • Author(s): 信夫愛、李秀栄、杉田有治
  • Organizer: 第60回日本生物物理学会年会
  • Invited
• [Presentation] Structure modeling of protein complex from experimental data using molecular dynamics simulation (2022)
  • Author(s): 森貴治
  • Organizer: 第60回日本生物物理学会年会
  • Invited
• [Presentation] Development of QM/MM methods and applications to chemical reactions of biomolecules (2022)
  • Author(s): Kiyoshi Yagi
  • Organizer: Tokyo Metropolitan University, Mini workshop
  • Int'l Joint Research / Invited
• [Presentation] Searching for the Structure of a Capped Pentapeptide, SIVSF, Using a Similarity Score of Infrared Spectra (2022)
  • Author(s): Kiyoshi Yagi
  • Organizer: 3rd International Symposium of JSPS Core-to-Core Program on "Molecular Recognition Mechanism between Flexible Molecules"
  • Int'l Joint Research / Invited
• [Presentation] Free Energy Perturbation Method in GENESIS (2022)
  • Author(s): 尾嶋拓, 杉田有治
  • Organizer: CBI学会2022年大会
• [Presentation] 非調和性を考慮した振動スペクトル計算法の開発と応用 (2022)
  • Author(s): 八木清
  • Organizer: 日本分光学会年次講演会
  • Invited
• [Presentation] MD-based inference of conformationoal ensemble from cryo-EM particle images (2022)
  • Author(s): Mao Oide
  • Organizer: 第9回「富岳」を中核とするHPCIシステム利用研究課題成果報告会
  • Invited
• [Presentation] 拡張アンサンブル法による生態分子動態の解析 (2022)
  • Author(s): 大出真央
  • Organizer: 第9回「富岳」を中核とするHPCIシステム利用研究課題成果報告会
  • Invited
• [Presentation] Anharmonic Vibrational Analyses of Bacteriorhodopsin by QM/MM Calculations (2022)
  • Author(s): Kiyoshi Yagi
  • Organizer: 19th International Conference on Retinal Protein
  • Int'l Joint Research
• [Presentation] Development of QM/MM methods and applications to chemical reactions of biomolecules (2022)
  • Author(s): 八木清
  • Organizer: 八木清
  • Invited
• [Presentation] 細胞内環境の生物物理学 (2022)
  • Author(s): 杉田有治
  • Organizer: 東京大学理学部物理コロキウム
  • Invited
• [Presentation] 新型コロナウイルススパイクタンパク質の糖鎖による構造安定性 (2022)
  • Author(s): 杉田有治
  • Organizer: 第19回糖鎖科学コンソーシアムシンポジウム
  • Invited
• [Presentation] Computational studies of conformational dynamics of membrane transporters and pumps (2022)
  • Author(s): Yuji Sugita
  • Organizer: 10th Asian Biological Inorganic Chemistry Conference
  • Int'l Joint Research / Invited
• [Presentation] Multi-Scale Molecular Dynamics Simulations to Study Repulsive Interactions in Regulating Biomolecular Condensation (2022)
  • Author(s): Cheng Tan
  • Organizer: The 32nd Tokyo RNA Club
  • Invited
• [Presentation] 静電相互作用の計算コストを抑えた自由エネルギー摂動法の開発 (2022)
  • Author(s): 尾嶋拓, 杉田有治
  • Organizer: 第36回分子シミュレーション討論会
• [Presentation] Implementation of residue level coarse-grained models in GENESIS for large-scale molecular dynamics simulations (2022)
  • Author(s): Cheng Tan
  • Organizer: 第36回分子シミュレーション討論会
• [Presentation] Protein structure determination by NMR: conformational multiplicity and the effects of macromolecular crowding (2022)
  • Author(s): Yutaka Ito
  • Organizer: The 7th International Symposium on Drug Discovery and Design by NMR
  • Int'l Joint Research / Invited
• [Presentation] Solution NMR approaches to 3D structure determination of proteins in living cells (2022)
  • Author(s): Yutaka Ito
  • Organizer: The Protein Society Webinar “Exploring Proteins in Living Cells”
  • Int'l Joint Research / Invited
• [Presentation] 常磁性ランタノイド金属を用いた蛋白質の溶液NMRおよびin-cell NMR解析 (2022)
  • Author(s): 伊藤 隆
  • Organizer: 第1回生命金属科学シンポジウム
  • Invited
• [Presentation] Protein behaviours under intracellular crowding environments (2022)
  • Author(s): Yutaka Ito
  • Organizer: TMU Workshop on Protein NMR
  • Invited
• [Presentation] シアノバクテリアの光センサーにおける脱プロトン化した塩基性アミノ酸の観測 (2022)
  • Author(s): 永江 峰幸，飯塚 佑介，青山 洋史，宮ノ入 洋平，神野 智司，伊藤 隆，広瀬 侑，三島 正規
  • Organizer: 第61回NMR討論会
• [Presentation] NMR解析を用いた解糖系酵素PGKの環境適応的活性制御による解糖系調節機構 (2022)
  • Author(s): 八木 宏昌，葛西 卓磨，Elisa Rioual，池谷 鉄兵，木川 隆則
  • Organizer: 第61回NMR討論会
• [Presentation] NMR studies of a Drosophila adapter protein, Drk (2022)
  • Author(s): Sayeesh, PM, Teppei Ikeya, Haruka Sugasawa, Riki Watanabe, Yutaka Ito
  • Organizer: 第1回生命金属科学シンポジウム
• [Presentation] In-cell NMRによるlinear diubiquitinのin-situ立体構造解析 (2022)
  • Author(s): 屋部 祥大，田岸 亮馬，鴨志田 一，美川 務，猪股 晃介，池谷 鉄兵，伊藤 隆
  • Organizer: 第61回NMR討論会
• [Presentation] In-cell NMR によるKeap1/Nrf2系の研究 (2022)
  • Author(s): 豊田 芽生，猪股 晃介，末広 志織，島 海翔，池谷 鉄兵，鈴木 隆史，山本 雅之，伊藤 隆
  • Organizer: 第61回NMR討論会
• [Presentation] 常磁性 NMR を用いた根粒菌マルチドメイン蛋白質FixJの立体構造解析 (2022)
  • Author(s): 大久保 里佳，池谷 鉄兵，渡邉 吏輝，菱倉 直樹，三島 正規，猪股 晃介，小手石 泰康，澤井 仁美，城 宣嗣，伊藤 隆
  • Organizer: 第61回NMR討論会
• [Presentation] マルチドメイン蛋白質GRB2とSOS1-PRM領域の相互作用解析 (2022)
  • Author(s): 館野 桂太，菅澤 はるか，安藤 考史，田端 真彩子，美川 務，猪股 晃介，甲斐荘 正恒，三島 正規，杉田 有治，池谷 鉄兵，伊藤 隆
  • Organizer: 第61回NMR討論会
• [Presentation] 常磁性NMRを用いたマルチドメイン蛋白質GRB2の立体構造解析 (2022)
  • Author(s): 安藤 考史，菅澤 はるか，館野 桂太，田端 真彩子，美川 務，宮野入 洋平，川端 庸平，Hisham Dokainish，Weitong Ren，大出 真央，寺内 勉，猪股 晃介，三島 正規，甲斐荘 正恒，杉田 有治，池谷 鉄兵，伊藤 隆
  • Organizer: 第61回NMR討論会
• [Presentation] GMPPNP結合型K-RasG12VとRgl2RBDの相互作用解析 (2022)
  • Author(s): 富樫 直之，宮田 裕貴，亀井 駿，菅澤 はるか，美川 務，猪股 晃介，田仲 加代子，伊藤 隆，池谷 鉄兵
  • Organizer: 第61回NMR討論会
• [Presentation] Stability and interaction of macromolecules altered by nucleoside triphosphates in cellular crowding (2022)
  • Author(s): 優乙石, 山崎竜人, Feig Michael, 杉田有治
  • Organizer: 第60回生物物理学会年会
• [Presentation] Microscopic Investigation on the Protein Aggregation Inhibition by ATP in Cell (2022)
  • Author(s): 優乙石, 杉田有治
  • Organizer: 第9回HPCIシステム利用研究課題 成果報告会
• [Presentation] Multi-scale simulations of large biological systems on Fugaku (2022)
  • Author(s): Yuji Sugita
  • Organizer: R-CCS symposium
  • Int'l Joint Research / Invited
• [Presentation] Reduced efficacy of a Src kinase inhibitor in crowded protein solution (2022)
  • Author(s): Yuji Sugita
  • Organizer: Prof. Sihyun Ham Memorial Symposium
  • Int'l Joint Research / Invited
• [Presentation] 高速QM/MM計算の開発と 生体分子ダイナミクスへの応用 (2022)
  • Author(s): 八木清
  • Organizer: 第35回日本放射光学会年会・放射光科学合同シンポジウム
  • Invited
• [Presentation] Development of GENESIS MD software on Fugaku supercomputer for understanding large scale biomolecular phenomena in cellular environments (2021)
  • Author(s): Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
  • Organizer: Pachifichem symposium
  • Int'l Joint Research / Invited
• [Presentation] Finding the reaction path of metalloenzyme using QM/MM in GENESIS (2021)
  • Author(s): Kiyoshi Yagi, Yuji Sugita
  • Organizer: Pachifichem symposium (#83)
  • Int'l Joint Research / Invited
• [Presentation] Anharmonic vibrational calculations of hydrogen bond network in protein using vibrational quasi-degenerate perturbation theory with localized coordinates (2021)
  • Author(s): Kiyoshi Yagi
  • Organizer: Pachifichem symposium (#410)
  • Int'l Joint Research / Invited
• [Presentation] How macromolecular crowding environments affect protein-ligand binding kinetics and thermodynamics (2021)
  • Author(s): Yuji Sugita
  • Organizer: Pachifichem symposium (#200)
  • Int'l Joint Research / Invited
• [Presentation] Molecular mechanisms for conformational changes and chemical reactions in the Ca2+-ATPase (2021)
  • Author(s): Yuji Sugita
  • Organizer: Pachifichem symposium (#206)
  • Int'l Joint Research / Invited
• [Presentation] Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems (2021)
  • Author(s): Jaewoon Jung, 笠原健人, 小 林千草, 尾嶋拓, 森貴治, 杉田有治
  • Organizer: 第 35 回分子シミュレーション討論会
• [Presentation] Capturing drastic state transitions of biological macromolecules by molecular dynamics simulation and nonlinear dimensionality reduction (2021)
  • Author(s): 大出真央, 杉田有治
  • Organizer: 第59回日本生物物理学会年会
• [Presentation] Extensive Sampling of Spike protein down, one-up, one-open, and two-up-like Conformations and Transitions in SARS-Cov-2 (2021)
  • Author(s): Hisham Dokainish
  • Organizer: 第59回日本生物物理学会年会
• [Presentation] Cryo-EM flexible fitting refinement with automatic error fixing for de novo protein structure modeling (2021)
  • Author(s): 森貴治、寺師玄記、松岳大輔、木原大亮、杉田有治
  • Organizer: 第59回日本生物物理学会年会
• [Presentation] Mechanisms for conformational changes of proteins upon ligand bindings (2021)
  • Author(s): Yuji Sugita
  • Organizer: 第59回日本生物物理学会年会
  • Invited
• [Presentation] Parallel computing algorithms in molecular dynamics simulations for extremely large-scale biological systems (2021)
  • Author(s): Yuji Sugita
  • Organizer: HITS Colloquium
  • Int'l Joint Research / Invited
• [Presentation] Weight average法による振動スペクトル計算と生体分子への応用 (2021)
  • Author(s): 八木清
  • Organizer: 第2回分子集合系計算科学セミナー
  • Invited
• [Presentation] Mechanisms for conformational changes of proteins upon ligand bindings (2021)
  • Author(s): Yuji Sugita
  • Organizer: Polish-Korean Protein Folding Conference
  • Int'l Joint Research / Invited
• [Presentation] QM/MM法の開発と生体分子の化学反応解析 (2021)
  • Author(s): 八木清
  • Organizer: 化学反応経路探索のニューフロンティア2021
  • Invited
• [Presentation] Enhanced Sampling Techniques (2021)
  • Author(s): Yuji Sugita
  • Organizer: CECAM CHARMM-GUI Workshop
  • Int'l Joint Research / Invited
• [Presentation] Procedures to obtain reliable free-energy profiles of conformational changes in membrane transporters (2021)
  • Author(s): Yuji Sugita
  • Organizer: ACS Fall 2021
  • Int'l Joint Research / Invited
• [Presentation] 量子化学と分子動力学の融合が拓く高分子の分子機能解析 (2021)
  • Author(s): 八木清
  • Organizer: 第1回溶液化学夏季講演会
  • Invited
• [Presentation] 分子動力学シミュレーションによる蛋白質の動的構造と基質結合：分子混雑環境の影響とSARS-CoV-2スパイク蛋白質に関する計算 (2021)
  • Author(s): 杉田有治
  • Organizer: 構造活性フォーラム2021
  • Invited
• [Presentation] 分子動力学計算プログラムGENESISにおけるQM/MM法の開発と応用 (2021)
  • Author(s): 八木清、杉田有治
  • Organizer: 第23回理論化学討論会
• [Presentation] Conformational flexibility and stability of SARS-CoV-2 spike protein in solution (2021)
  • Author(s): Yuji Sugita
  • Organizer: ACS Spring 2021
  • Int'l Joint Research / Invited
• [Presentation] Solution NMR approaches to 3D structure determination of proteins in living eukaryotic cells (2021)
  • Author(s): Yutaka Ito, Kohsuke Inomata, Teppei Ikeya
  • Organizer: 22nd International Society of Magnetic Resonance Conference (ISMAR)
  • Int'l Joint Research / Invited
• [Presentation] 複数の異なる NMR データの統合解析によるタンパク質 multi-state 立体構造解析 (2021)
  • Author(s): 池谷 鉄兵，伊藤 隆
  • Organizer: 第21回日本蛋白質科学会年会
  • Invited
• [Presentation] Multi-state structure determination and dynamics analysis reveals a new ubiquitin-recognition mechanism in yeast ubiquitin C-terminal hydrolase (2021)
  • Author(s): Teppei Ikeya, Mayu Okada, Yutaka Tateishi, Eri Nojiri, Tsutomu Mikawa, Sundaresan Rajesh, Hiroki Ogasa, Takumi Ueda, Hiromasa Yagi, Toshiyuki Kohno, Takanori Kigawa, Ichio Shimada, Peter Guentert, Yutaka Ito
  • Organizer: 22nd International Society of Magnetic Resonance Conference (ISMAR)
  • Int'l Joint Research
• [Presentation] Insight into the C-terminal SH3 mediated binding of Drosophila Drk towards Sos and Dos (2021)
  • Author(s): Sayeesh. P. M., Teppei Ikeya, Haruka Sugasawa, Riki Watanabe, Yutaka Ito
  • Organizer: 22nd International Society of Magnetic Resonance Conference (ISMAR)
  • Int'l Joint Research
• [Presentation] Molecular mechanism of glycolytic flux control intrinsic to human phosphoglycerate kinase (2021)
  • Author(s): Hiromasa Yagi, Takuma Kasai, Elisa Rioual, Teppei Ikeya, Taganori Kigawa
  • Organizer: 第59回日本生物物理学会
• [Presentation] Insight into the C-terminal SH3 mediated binding of Drosophila Drk towards Sos and Dos (2021)
  • Author(s): Sayeesh. P. M., Teppei Ikeya, Haruka Sugasawa, Riki Watanabe, Yutaka Ito
  • Organizer: 第44回日本分子生物学会
• [Presentation] NMRによるKRASとRGL2の相互作用解析 (2021)
  • Author(s): 富樫直之，亀井駿，菅澤はるか，猪股晃介，伊藤隆，田仲加代子，池谷鉄兵
  • Organizer: 第44回日本分子生物学会
• [Presentation] 直鎖状ユビキチン二量体の溶液構造解析 (2021)
  • Author(s): 屋部 祥大，田岸亮馬，鴨志田一，美川務，猪股晃介，池谷鉄兵，伊藤隆
  • Organizer: 第44回日本分子生物学会
• [Presentation] In-cell NMRを用いたKeap1-Nrf2制御系の解析 (2021)
  • Author(s): 末広志織，猪股晃介，豊田芽生，池谷鉄兵，鈴木隆史，山本 雅之，伊藤隆
  • Organizer: 第44回日本分子生物学会
• [Presentation] Development of Trajectory Analyzer for Cellular-Scale Molecular Dynamics Simulations (2021)
  • Author(s): 優乙石, 杉田有治
  • Organizer: 第59回日本生物物理学会
• [Presentation] In situ Analysis of Protein Dynamics with All atom Cytoplasm Simulations (2021)
  • Author(s): 優乙石, Po-hung Wang , 杉田有治
  • Organizer: 第８回HPCIシステム利用研究課題 成果報告会
• [Presentation] 富岳を用いた新型コロナウイルス 表面のスパイクタンパク質動的構造予測 (2021)
  • Author(s): 杉田 有治
  • Organizer: 近畿化学協会コンピュータ化学部会
  • Invited
• [Presentation] 新型コロナウイルス 表面のタンパク質動的構造予測 (2021)
  • Author(s): 杉田 有治
  • Organizer: HPCIフォーラム
  • Invited
• [Presentation] Intrinsic Conformational Flexibility of SARS-CoV-2 Spike-Protein Simulated on Fugaku (2021)
  • Author(s): Yuji Sugita
  • Organizer: The 3rd R-CCS International Symposium
  • Int'l Joint Research / Invited
• [Presentation] Multi-scale MD simulations using GENESIS on Fugaku (2021)
  • Author(s): Yuji Sugita
  • Organizer: The 1st Fugaku Bio-supercomputing Workshop on Cellular-Scale Molecular Dynamics Simulations
  • Int'l Joint Research / Invited
• [Presentation] スーパーコンピュータが明らかにする蛋白質の動的構造と機能 (2020)
  • Author(s): 杉田 有治
  • Organizer: 理研・東北大学連携シンポジウム「計測科学が拓く生命科学の新展開」
  • Invited
• [Presentation] 大規模QM/MM計算が拓く生命科学のフロンティア (2020)
  • Author(s): 八木 清
  • Organizer: 第1回ピコバイオロジー研究会
  • Invited
• [Presentation] Development of GENESIS on Fugaku supercomputer and its application of Spike protein on the surface of SARS-CoV-2 in solution (2020)
  • Author(s): Jaewoon Jung
  • Organizer: HPCIC計算科学フォーラム
  • Invited
• [Presentation] 計算機シミュレーションで細胞の中を観る (2020)
  • Author(s): 杉田 有治
  • Organizer: 京都大学MACSコロキアム
  • Invited
• [Presentation] 細胞環境はどのようにタンパク質の構造・ダイナミクス・機能に影響を与えるか？ (2020)
  • Author(s): 杉田 有治
  • Organizer: CBI学会2020年大会
  • Invited
• [Presentation] All-atom molecular dynamics simulations of spike protein on the surface of SARS-CoV-2 in solution (2020)
  • Author(s): Yuji Sugita
  • Organizer: RIKEN-NRC HPC Workshop
  • Int'l Joint Research / Invited
• [Presentation] 新型コロナウイルス表面のタンパク質動的構造予測 (2020)
  • Author(s): 杉田 有治
  • Organizer: 第9回JCAHPCセミナー
  • Invited
• [Presentation] Theoretical Study on the Transport Cycle of the Heme ABC Transporter BhuUV-T (2020)
  • Author(s): 田村康一
  • Organizer: 第58回生物物理学会年会
  • Invited
• [Presentation] Rational design of membrane-spanning alpha-helical peptide barrels (2020)
  • Author(s): Ai Niitsu
  • Organizer: 第58回生物物理学会年会
  • Invited
• [Presentation] Multi-state protein structure determination by integrated analysis of several NMR data sets (2020)
  • Author(s): 池谷鉄兵，伊藤 隆
  • Organizer: 第58回生物物理学会年会
  • Invited
• [Presentation] 計算化学と振動分光の融合による高分子内分子動態解析法の開発と応用 (2020)
  • Author(s): 八木清
  • Organizer: 第69回高分子討論会
  • Invited
• [Presentation] Use of enhanced conformational sampling for the analysis of protein-ligand binding processes (2020)
  • Author(s): Yuji Sugita
  • Organizer: Telluride Summer Research Conference
  • Int'l Joint Research / Invited
• [Presentation] Developments and applications of generalized-ensemble methods for free-energy analysis of protein-ligand binding (2020)
  • Author(s): Hiraku Oshima
  • Organizer: 第20回日本蛋白質科学会年会
  • Invited
• [Presentation] NMR studies on the protonation state of cyanobacteriochrome (2020)
  • Author(s): 三島正規
  • Organizer: 第59回NMR討論会
• [Presentation] NMRを用いたアダプター蛋白質Drkの動態解析 (2020)
  • Author(s): 渡邉吏輝，プバティ マキシン サイーシュ，末元雄介，木川隆則，三島正規，猪股晃介，池谷鉄兵，伊藤 隆
  • Organizer: 第59回NMR討論会
• [Presentation] PRE，PCSを用いたマルチドメイン蛋白質GRB2の立体構造解析 (2020)
  • Author(s): 田端真彩子，池谷鉄兵，美川 務，川端庸平，安藤考史，館野桂太，三島正規，伊藤 隆
  • Organizer: 第59回NMR討論会
• [Presentation] タンパク質 リガンド結合の自由エネルギー計算法の開発と応用 (2020)
  • Author(s): 尾嶋拓
  • Organizer: CBI学会2020年大会
• [Presentation] 高速クライオ電顕フィッティング法の開発と応用 (2020)
  • Author(s): 森貴治
  • Organizer: CBI学会2020年大会
• [Presentation] Reduced protein-protein interactions in the cellular crowding with binding of nucleoside triphosphates (2020)
  • Author(s): 優乙石, Michael Feig, 杉田有治
  • Organizer: 第58回生物物理学会年会
• [Presentation] 高度細胞機能を解析する分子動態計測と情報科学との融合 (2020)
  • Author(s): 伊藤 隆
  • Organizer: 日本化学会第100春季年会
  • Invited
• [Presentation] 生細胞内のタンパク質立体構造解析 (2020)
  • Author(s): 池谷鉄兵，伊藤 隆，他
  • Organizer: 日本化学会第100春季年会
  • Invited
• [Presentation] All-atom molecular dynamics simulation of the altered protein-protein interaction with metabolites and ions in the cytoplasm. (2020)
  • Author(s): Isseki Yu
  • Organizer: Biophysical Society 64th Annual Meeting
  • Int'l Joint Research
• [Presentation] Free-Energy Landscape of Protein-Ligand Binding by generalized REST (2019)
  • Author(s): Yuji Sugita
  • Organizer: 257th ACS national meeting
  • Int'l Joint Research / Invited
• [Presentation] スパコン「京」とGENESISを用いた創薬自由エネルギー計算 (2019)
  • Author(s): 杉田有治, 李秀栄
  • Organizer: 第4回理研ー製薬協連携フォーラム「創薬専用MDシミュレーターの産学共同開発」
  • Invited
• [Presentation] Simulations of Biomolecules in Cellular Crowded Environments (2019)
  • Author(s): Yuji Sugita
  • Organizer: Albany 2019. the 20th Conversation
  • Int'l Joint Research / Invited
• [Presentation] Free-Energy Calculations of Protein-Ligand Binding in Solution and in Cellular Environments (2019)
  • Author(s): Yuji Sugita
  • Organizer: Free Energy Workshop
  • Int'l Joint Research / Invited
• [Presentation] Protein-protein and protein-ligand interaction in cellular environments (2019)
  • Author(s): Yuji Sugita
  • Organizer: PSSJ 19th Annual Symposium
  • Invited
• [Presentation] Slow-down of protein and metabolite diffusion in crowded protein solution", TSRC workshop on macromolecular crowding (2019)
  • Author(s): Yuji Sugita
  • Organizer: Telluride Summer Conference
  • Int'l Joint Research / Invited
• [Presentation] Free-Energy Calculations of Protein-Ligand Binding by Enhanced Sampling Methods (2019)
  • Author(s): Yuji Sugita
  • Organizer: The 10th Toyota RIKEN International Workshop on Science of Life Phenomena Woven by Water and Biomolecules
  • Int'l Joint Research / Invited
• [Presentation] Machine learning approach to link MD simulation with single-molecule experiment for understanding protein folding and dynamics (2019)
  • Author(s): Yuji Sugita
  • Organizer: The 5th Korean-Polish Conference on "Protein Folding: Theoretical and Experimental Approaches
  • Int'l Joint Research / Invited
• [Presentation] Enhanced Conformational Sampling Methods for Free Energy Calculation (2019)
  • Author(s): Yuji Sugita
  • Organizer: CHARMM-GUI Workshop
  • Int'l Joint Research / Invited
• [Presentation] 分子動力学で見る細胞質内での分子の動き (2019)
  • Author(s): 杉田有治
  • Organizer: Chemical Probe第二回合同合宿セミナー
  • Invited
• [Presentation] Large-scale molecular dynamics simulation of biomolecules in cellular environments (2019)
  • Author(s): Yuji Sugita
  • Organizer: Accelerated Data Analytics and Computing Workshop 8
  • Int'l Joint Research / Invited
• [Presentation] Free-Energy Calculations of Protein-Ligand Binding using GENESIS software (2019)
  • Author(s): Yuji Sugita
  • Organizer: ICMS2019
  • Int'l Joint Research / Invited
• [Presentation] Molecular Dynamics and Interaction of Protein-Ligand Binding in Crowded Cellular Environments (2019)
  • Author(s): Yuji Sugita
  • Organizer: the 42th Annual Meeting of the Molecular Biology Society of Japan
  • Invited
• [Presentation] Free-Energy Calculations of Protein-Ligand Binding using GENESIS (2019)
  • Author(s): Yuji Sugita
  • Organizer: Supercomputer Symposium at IMS
  • Invited
• [Presentation] Solution NMR approaches to 3D structure determination of proteins in living eukaryotic cells (2019)
  • Author(s): Yutaka Ito, Teppei Ikeya
  • Organizer: 33rd Annual Symposium of the Protein Society, USA
  • Int'l Joint Research / Invited
• [Presentation] High resolution protein 3D structure determination in living eukaryotic cells (2019)
  • Author(s): Teppei Ikeya, Yutaka Ito
  • Organizer: The 8th Asia Pacific NMR Symposium, Singapore
  • Int'l Joint Research / Invited
• [Presentation] Multi-state protein structure determination by integrated analysis of several NMR data sets (2019)
  • Author(s): Teppei Ikeya, Yutaka Ito
  • Organizer: IPR seminar
  • Int'l Joint Research / Invited
• [Presentation] High-resolution protein 3D structure determination in living eukaryotic cells (2019)
  • Author(s): Takashi Tanaka, Yutaka Ito, et al.
  • Organizer: The 12th Australian and New Zealand Society for Magnetic Resonance Conference (ANZMAG conference 2019)
  • Int'l Joint Research / Invited
• [Presentation] MDシミュレーション vs NMR立体構造計算(multi-state立体構造計算) (2019)
  • Author(s): 池谷鉄兵，伊藤 隆
  • Organizer: 第20回若手NMR研究会
  • Invited
• [Presentation] 溶液NMRを用いたin situ構造生物学 (2019)
  • Author(s): 伊藤 隆，池谷鉄兵
  • Organizer: 第13回バイオ関連化学シンポジウム2019
  • Invited
• [Presentation] 常磁性効果による遠距離構造情報を利用したタンパク質multi-state立体構造解析 (2019)
  • Author(s): 池谷鉄兵，伊藤 隆，他
  • Organizer: 第58回NMR討論会（2019）
  • Invited
• [Presentation] Solution NMR approaches to 3D structure determination of proteins in living eukaryotic cells (2019)
  • Author(s): Yutaka Ito, Teppei Ikeya
  • Organizer: The 42th Annual Meeting of the Molecular Biology Society of Japan
  • Invited
• [Presentation] All-atom molecular dynamics simulation of the reduced protein-protein interaction with metabolites in the cytoplasm. (2019)
  • Author(s): Isseki Yu
  • Organizer: 第57回日本生物物理学会年会
• [Presentation] 細胞質中の代謝物によって改変される蛋白質間相互作用の全原子分子動力学シミュレーション (2019)
  • Author(s): 優 乙石
  • Organizer: 第33回 分子シミュレーション討論会
• [Book] イメージング時代の構造生命科学 (2020)
  • Author(s): 田中 啓二、若槻 壮市
  • Total Pages: 248
  • Publisher: 羊土社
  • ISBN: 9784758103855
• [Book] In-cell NMR Spectroscopy: From Molecular Sciences to Cell Biology (2019)
  • Author(s): Yuji Sugita, Michael Feig
  • Total Pages: 305
  • Publisher: Royal Society of Chemistry
  • ISBN: 9781788012171
• [Book] Biomolecular Simulation: Methods and Protocols (2019)
  • Author(s): Yuji Sugita, Motoshi Kamiya, Hiraku Oshima, Suyong Re
  • Total Pages: 578
  • Publisher: Springer
  • ISBN: 9781493996070
• [Remarks] 理化学研究所開拓研究本部杉田理論分子科学研究室
  • URL: https://tms.riken.jp/
• [Remarks] 東京都立大学化学科有機構造生物化学研究室
  • URL: https://www.comp.tmu.ac.jp/osbc/Group_Ito/index.html