研究業績
論文
44. Ikuo Fukuda, Kei Moritsugu, Junichi Higo, Yoshifumi Fukunishi, "A Cutoff-based Method with Charge-distribution-data Driven Pair Potentials for Efficiently Estimating Electrostatic Interactions in Molecular System", Journal of Chemical Physics (2023) 159: 234116.
43. Kei Moritsugu, Akinori Kidera, Toru Ekimoto and Mitsunori Ikeguchi, “Binding and unbinding pathways of peptide substrate on SARS-CoV-2 3CL protease“, Journal of Chemical Information and Modeling (2023) 63: 240-250.
42. Yusuke Kanematsu , Akihiro Narita , Toshiro Oda , Ryotaro Koike , Motonori Ota , Yu Takano , Kei Moritsugu , Ikuko Fujiwara , Kotaro Tanaka , Hideyuki Komatsu , Takayuki Nagae , Nobuhisa Watanabe , Mitsusada Iwasa , Yuichiro Maéda , Shuichi Takeda, “ Structures and mechanisms of the actin ATP hydrolysis“, Proceedings of the National Academy of Sciences (2022) 119: e2122641119.
41. Akinori Kidera, Kei Moritsugu, Toru Ekimoto and Mitsunori Ikeguchi, "Functional Dynamics of SARS-CoV-2 3C-like protease as a member of clan PA", Biophysical Reviews (2022) 14, 1473–1485.
40. Akinori Kidera, Kei Moritsugu, Toru Ekimoto and Mitsunori Ikeguchi, “Allosteric regulation of 3CL protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble“, Journal of Molecular Biology (2021) 433: 167324.
39. Keijun Kakihara, Kengo Asamizu, Kei Moritsugu, Masahide Kubo, Tetsuya Kitaguchi, Akinori Endo, Akinori Kidera, Mitsunori Ikeguchi, Akira Kato, Masayuki Komada and Toshiaki Fukushima, “The molecular basis of ubiquitin-specific protease 8 autoinhibition by the WW-like domain“, Communications Biology (2021) 4: 1272.
38. Kei Moritsugu, “ Multiscale enhanced sampling using machine learning“, Life (2021) 11: 1076.
37. Ikuo Fukuda and Kei Moritsugu, “Analysis of multiple data sequences with different distributions: defining common principal component axes by ergodic sequence generation and multiple reweighting composition“, IOP SciNotes (2021) 2: 035201.
36. Kei Moritsugu, Koh Takeuchi, Narutoshi Kamiya, Junichi Higo, Isao Yasumatsu, Yoshifumi Fukunishi and Ikuo Fukuda, “Flexibility and cell permeability of cyclic Ras–inhibitor peptides revealed by coupled Nosé–Hoover equation”, Journal of Chemical Information and Modeling (2021) 61: 1921-1930.
35. Kei Moritsugu, Norifumi Yamamoto, Yasushige Yonezawa, Shin-ichi Tate, and Hiroshi Fujisaki, “Path ensembles for Pin1-catalyzed cis-trans isomerization of a substrate calculated by weighted ensemble simulations”, Journal of Chemical Theory and Computation (2021) 17: 2522–2529.
34. Ikuo Fukuda, Kei Moritsugu and Yoshifumi Fukunishi, “On ergodicity for multi-dimensional harmonic oscillator systems with Nose-Hoover type thermostat”, Regular and Chaotic Dynamics (2021) 26: 183-204.
33. Kei Moritsugu, Yoshihiko Nishino and Akinori Kidera, “Inter-lobe motions allosterically regulate the function of EGFR kinase: Comparative study of crystal structures and molecular simulations”, Journal of Molecular Biology (2020) 432: 4561-4575.
32. Ikuo Fukuda and Kei Moritsugu, “Temperature-Energy-space Sampling Molecular Dynamics: Deterministic, Iteration-free, and Single-replica Method utilizing Continuous Temperature System”, Journal of Physics A (2020) 53: 375004.
31. Kei Moritsugu, Tsubasa Ito and Akinori Kidera, "Allosteric response to ligand binding: Molecular dynamics study of the N-terminal domains in IP3 receptor ", Biophysics and Physicobiology (2019) 16: 232-239.
30. Kei Moritsugu, Hafumi Nishi, Keiichi Inariyama, Masanori Kobayashi and Akinori Kidera, "Dynamic recognition and linkage specificity in K63 di-ubiquitin and TAB2 NZF domain complex", Scientific Reports (2018) 8: 16478.
29. Hiroshi Fujisaki, Kei Moritsugu, Ayori Mitsutake, and Hiromichi Suetani, ”Conformational change of a biomolecule studied by the weighted ensemble method: Use of the diffusion map method to extract reaction coordinates”, Journal of Chemical Physics (2018) 149: 134112.
28. Kei Moritsugu, Tohru Terada, Hironori Kokubo, Satoshi Endo, Toshimasa Tanaka and Akinori Kidera, "Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion", Journal of Chemical Physics (2018) 149: 072314.
27. Yasuhiro Matsunaga, Tsutomu Yamane, Tohru Terada, Kei Moritsugu, Hiroshi Fujisaki, Satoshi Murakami, Mitsunori Ikeguchi, and Akinori Kidera, “Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB”, eLIFE (2018) 7: e31715.
26. Satoshi Ishiyama, Atsuya Nishiyama, Yasushi Saeki, Kei Moritsugu, Daichi Morimoto, Luna Yamaguchi, Naoko Arai, Rumie Matsumura, Toru Kawakami, Yuichi Mishima, Hironobu Hojo, Shintaro Shimamura, Fuyuki Ishikawa, Shoji Tajima, Keiji Tanaka, Mariko Ariyoshi, Masahiro Shirakawa, Mitsunori Ikeguchi, Akinori Kidera, Isao Suetake, Kyohei Arita, and Makoto Nakanishi, “Structure of the H3 ubiquitin code/Dnmt1 reader module complex reveals the basis for DNA methylation maintenance”, Molecular Cell (2017) 68: 350-360.
25. Kei Moritsugu, Tohru Terada and Akinori Kidera, "Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes", Journal of Physical Chemistry B (2017) 121: 731-740.
24. Ikuo Fukuda and Kei Moritsugu, “Coupled Nosé-Hoover equations of motions without time scaling”, Journal of Physics A (2016) 50: 015002.
23. Kei Moritsugu, Tohru Terada and Akinori Kidera, "Multiscale enhanced sampling for protein systems: An extension via adiabatic separation", Chemical Physics Letters (2016) 661: 279-283.
22. Hideaki Shimojo, Ayumi Kawaguchi, Takashi Oda, Nobuto Hashiguchi, Satoshi Omori, Kei Moritsugu, Akinori Kidera, Kyoko Hiragami-Hamada, Jun-ichi Nakayama, Mamoru Sato and Yoshifumi Nishimura, “Extended string-like binding of the phosphorylated HP1α N-terminal tail to the lysine 9-methylated histone H3 tail”, Scientific Reports (2016) 6: 22527.
21. Ikuo Fukuda and Kei Moritsugu, “Coupled Nosé-Hoover Equations of Motions: coupling the physical system Nosé-Hoover equation and temperature system Nosé-Hoover equation”, Physics Reviews E (2016) 93: 033306.
20. Ikuo Fukuda and Kei Moritsugu, “Double density dynamics: realizing a joint distribution of a physical system and a parameter system”, Journal of Physics A (2015) 48: 455001.
19. Kei Moritsugu, Ryotaro Koike, Kouki Yamada, Hiroaki Kato and Akinori Kidera, “Motion Tree delineates hierarchical structure of protein dynamics observed in molecular dynamics simulation”, PLoS ONE (2015) 10: e0131583.
18. Kei Moritsugu, Tohru Terada and Akinori Kidera, “Energy Landscape of All-atom Protein-protein Interactions Revealed by Multiscale Enhanced Sampling”, PLoS Computational Biology (2014) 10: e1003901.
17. Kei Moritsugu, Tohru Terada and Akinori Kidera, “Multiscale Enhanced Sampling Driven by Multiple Coarse-grained Models”, Chemical Physics Letters (2014) 616–617, 20-24.
16. Kei Moritsugu, Akinori Kidera and Jeremy C. Smith, “Solvent Friction Effect Propagate over the Entire Protein Molecule through Low-Frequency Collective Modes”, Journal of Physical Chemistry B (2014) 118: 8559-8565.
15. Hiroshi Fujisaki, Motoyuki Shiga, Kei Moritsugu and Akinori Kidera, “Multiscale Enhanced Path Sampling Based on the Onsager-Machlup Action: Application to a Model Polymer”, Journal of Chemical Physics (2013) 139: 054117.
14. Dennis Glass, Kei Moritsugu, Xiaolin Cheng and Jeremy C. Smith, “REACH Coarse-Grained Simulation of a Cellulose Fiber”, Biomacromolecules (2012) 13: 2634- 2644.
13. Yasuhiro Matsunaga, Hiroshi Fujisaki, Tohru Terada, Tadaomi Furuta, Kei Moritsugu, and Akinori Kidera, “Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase”, PLoS Computational Biology (2012) 8: e1002555.
12. Kei Moritsugu, Tohru Terada and Akinori Kidera, “Disorder-to-order Transition of an intrinsically Disordered Region of Sortase Revealed by Multiscale Enhanced Sampling”, Journal of the American Chemical Society (2012) 134: 7094-7101.
11. Kei Moritsugu, Tohru Terada and Akinori Kidera, “Scalable Free Energy Calculation of Proteins via Multiscale Essential Sampling”, Journal of Chemical Physics (2010) 133: 224105.
10. Kei Moritsugu, Brigitte M. Njunda and Jeremy C. Smith, “Theory and Normal Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding”, Journal of Physical Chemistry B (2010) 114: 1479-1485.
9. Kei Moritsugu, Vandana Kurkal-Siebert, and Jeremy C. Smith, “REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics”, Biophysical Journal (2009) 97: 1158-1167.
8. Kei Moritsugu and Jeremy C. Smith, “REACH: A Program for Coarse-Grained Biomolecular Simulation”, Computer Physics Communications (2009) 180: 1188-1195.
7. Kei Moritsugu and Jeremy C. Smith, “REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Structural Classes”, Biophysical Journal (2008) 95: 1639-1648.
6. Kei Moritsugu and Jeremy C. Smith, “Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian”, Biophysical Journal (2007) 93: 3460-3469.
5. Kei Moritsugu and Jeremy C. Smith, “Temperature Dependent Protein Dynamics: A Simulation-Based Probabilistic Diffusion-Vibration Langevin Description”, Journal of Physical Chemistry B (2006) 110: 5807-5816.
4. Kei Moritsugu and Jeremy C. Smith, “Langevin Model of the Temperature and Hydration Dependence of Protein Vibrational Dynamics”, Journal of Physical Chemistry B (2005) 109: 12182-12194.
3. Kei Moritsugu and Akinori Kidera, “Protein Motions Represented by Moving Normal Mode Coordinates”, Journal of Physical Chemistry B (2004) 108: 3890-3898.
2. Kei Moritsugu, Osamu Miyashita and Akinori Kidera, “Temperature Dependence of Vibrational Energy Transfer in a Protein Molecule”, Journal of Physical Chemistry B (2003) 107: 3309-3317.
1. Kei Moritsugu, Osamu Miyashita and Akinori Kidera, “Vibrational Energy Transfer in a Protein Molecule”, Physical Review Letter (2000) 85: 3970-3973.
口頭発表（2022年から）
5. 森次 圭
「MSES法によるタンパク質の構造探索」
タンパク質の構造ダイナミクス研究会、横浜、2024年5月18日
4. 森次 圭
「生体分子に向けたシミュレーション法の開発とその応用研究」
スーパーコンピュータワークショップ2023、岡崎、2024年1月17日
3. 吉村 玲奈
「NRK によるCK2 活性制御の構造モデリングと解析」
第3 回 構造基盤創薬化学研究会、大阪、2024年1月10日
2. 森次 圭
「重み付きアンサンブル法によるプロテアーゼへの基質結合・解離シミュレーション」
第3 回 構造基盤創薬化学研究会、大阪、2024年1月10日
1. 森次 圭
「重み付きアンサンブル法と生体分子への応用」
第3回生体分子シミュレーション・モデリング研究会、函館、2022年10月1日
ポスター発表（2022年から)
8. Kenta Omoto, Kei Moritsugu
「Molecular Dynamics Simulation of Actin Filaments 」
第24回日本蛋白質科学会年会、札幌、2024年6月13日
7. Hiroto Terada, Kei Moritsugu
「Proposal of in silico screening protocol based on protein structural fluctuation and drug binding mode 」
第24回日本蛋白質科学会年会、札幌、2024年6月12日
6. Hiroto Terada, Kei Moritsugu
「Advance of in silico screening based on protein structural fluctuation and drug binding mode」
第61回日本生物物理学会年会、名古屋、2023年11月14日
5. Kenta Omoto, Kei Moritugu
「Structural samplings of actin that are dependent on the bound nucleotides」
第61回日本生物物理学会年会、名古屋、2023年11月14日
4. Rena Yoshimura, Beni Lestari, Toshiaki Fukushima, Kei Moritsugu
「Structural modeling and analysis of NRK-mediated regulation of CK2 activity」
第61回日本生物物理学会年会、名古屋、2023年11月14日
3. 森次 圭
「Minimum free energy path calculation for the structural change of ABC multi-drug efflux transporter」
第61回日本生物物理学会年会、名古屋、2023年11月14日
2. 森次 圭
「アクチンリン酸塩解離パスの構造揺らぎ依存性」
第10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、東京、2023年10月27日
1. 森次 圭
「Binding and unbinding kinetics of peptide substrate on SARS-CoV-2 3CL protease」
第60回日本生物物理学会年会、函館、2022年9月28-30日
総説、著書
6. 松永 康佑、森次 圭、藤崎 弘士、「タンパク質の構造変化をどのように記述するか―生体分子におけるパスサンプリング手法の発展」、日本物理学会誌 (2021) 76: 714-722.
5. Hiroshi Fujisaki, Kei Moritsugu and Yasuhiro Matsunaga, “Exploring configuration space and path space of biomolecules using enhanced sampling techniques: Searching for mechanism and kinetics of biomolecular functions”, International Journal of Molecular Sciences (2018) 19: 3177.
4. Hiroshi Fujisaki, Kei Moritsugu, Yasuhiro Matsunaga, Tetsuya Morishita, and Luca Maragliano, ”Extended phase-space methods for enhanced sampling in molecular simulations: a review”, Frontiers in Bioengineering and Biotechnology (2015) 3: 125.
3. 森次 圭、「マルチスケール手法によるタンパク質全原子構造サンプリング」分子シミュレーション研究会会誌“アンサンブル”(2014) 16: 227-233.
2. 森次 圭、「粗視化モデルを用いたマルチスケールシミュレーションシステムの構築」、生物物理学会誌 (2012) 52: 26-27.
1. Akinori Kidera, Kei Moristugu, Yasuhiro Matsunaga and Hiroshi Fujisaki, “Molecular Dynamics Simulation of Proteins: Two Models of Anharmonic Dynamics”, Proteins: Energy, Heat and Signal Flow, Chapter 5, CRC Press (2009), p107-127.