Publications
Original papers and others
Kazushi Okada, Takuma Kikutsuji, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi "Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach", arXiv: https://arxiv.org/abs/2402.08448
Tomoki Matsuda, Shinya Sakai, Kei-ichi Okazaki, Takeharu Nagai "Improvement of the Green–Red Förster Resonance Energy Transfer-Based Ca2+ Indicator by Using the Green Fluorescent Protein, Gamillus, with a Trans Chromophore as the Donor", ACS Sens. 9, 4, 1743–1748 (2024); https://doi.org/10.1021/acssensors.3c02398
Jun Ohnuki, Titouan Jaunet-Lahary, Atsuko Yamashita, and Kei-ichi Okazaki "Accelerated Molecular Dynamics and AlphaFold Uncover a Missing Conformational State of Transporter Protein OxlT ", J. Phys. Chem. Lett. 15, 725–732 (2024); https://doi.org/10.1021/acs.jpclett.3c03052
Maho Yagi-Utsumi, Haruko Miura, Christian Ganser, Hiroki Watanabe, Methanee Hiranyakorn, Tadashi Satoh, Takayuki Uchihashi, Koichi Kato, Kei-ichi Okazaki, and Kazuhiro Aoki “Molecular Design of FRET Probes Based on Domain Rearrangement of Protein Disulfide Isomerase for Monitoring Intracellular Redox Status”, Int. J. Mol. Sci. 2023, 24(16), 12865; https://doi.org/10.3390/ijms241612865
Titouan Jaunet-Lahary, Tatsuro Shimamura, Masahiro Hayashi, Norimichi Nomura, Kouta Hirasawa, Tetsuya Shimizu, Masao Yamashita, Naotaka Tsutsumi, Yuta Suehiro, Keiichi Kojima, Yuki Sudo, Takashi Tamura, Hiroko Iwanari, Takao Hamakubo, So Iwata, Kei-ichi Okazaki, Teruhisa Hirai, Atsuko Yamashita “Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota”, Nat. Commun. 14, 1730 (2023) https://doi.org/10.1038/s41467-023-36883-5
Ryohei Kobayashi, Hiroshi Ueno, Kei-ichi Okazaki & Hiroyuki Noji “Molecular mechanism on forcible ejection of ATPase inhibitory factor 1 from mitochondrial ATP synthase”, Nat. Commun. 14, 1682 (2023) https://doi.org/10.1038/s41467-023-37182-9
Shi-Jie Chen, Mubashir Hassan, Robert L Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin S Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, George D Rose “Opinion: Protein folds vs. protein folding: Differing questions, different challenges” Proc. Natl. Acad. Sci. USA 120 (1), e2214423119 (2023); https://doi.org/10.1073/pnas.2214423119
Takuma Kikutsuji, Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, and Nobuyuki Matubayasi “Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)”, J. Chem. Phys. 156, 154108 (2022); https://doi.org/10.1063/5.0087310
Md. Iqbal Mahmood, Adolfo B. Poma, and Kei-ichi Okazaki "Optimizing Gō‐MARTINI coarse‐grained model for F-BAR protein on lipid membrane", Front. Mol. Biosci. 8, 619381, https://doi.org/10.3389/fmolb.2021.619381 (2021)
Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, and Nobuyuki Matubayasi “Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide”, J. Chem. Phys. 153, 054115, https://doi.org/10.1063/5.0009066 (2020)
Kei-ichi Okazaki, Akihiko Nakamura, and Ryota Iino “Chemical-State-Dependent Free Energy Profile from Single-Molecule Trajectories of Biomolecular Motors: Application to Processive Chitinase”, J. Phys. Chem. B 124, 30, 6475−6487, https://doi.org/10.1021/acs.jpcb.0c02698 (2020)
Judith Warnau, David Wöhlert, Kei-ichi Okazaki, Özkan Yildiz, Ana P. Gamiz-Hernandez, Ville R. I. Kaila, Werner Kühlbrandt and Gerhard Hummer “Ion Binding and Selectivity of the Na+/H+ Antiporter MjNhaP1 from Experiment and Simulation”, J. Phys. Chem. B 124, 2, 336-344, https://doi.org/10.1021/acs.jpcb.9b08552 (2020)
Md. Iqbal Mahmood, Hiroshi Noguchi and Kei-ichi Okazaki “Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations”, Sci. Rep., 9, 14557 (11 pages), https://doi.org/10.1038/s41598-019-51202-z (2019)
Kei-ichi Okazaki, David Wöhlert, Judith Warnau, Hendrik Jung, Özkan Yildiz, Werner Kühlbrandt and Gerhard Hummer “Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting”, Nature Communications 10, 1742 (10 pages), https://doi.org/10.1038/s41467-019-09739-0 (2019)
PaNhaP-TPS.mp4
Akihiko Nakamura, Kei-ichi Okazaki, Tadaomi Furuta, Minoru Sakurai and Ryota Iino “Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin”, Nat. Commun. 9, 3814 (12 pages), DOI:10.1038/s41467-018-06362-3 (2018)
Hendrik Jung, Kei-ichi Okazaki and Gerhard Hummer “Transition path sampling of rare events by shooting from the top” J. Chem. Phys. 147: 152716 (10 pages), DOI: 10.1063/1.4997378 (2017)
Mitsuhiro Sugawa, Kei-ichi Okazaki, Masaru Kobayashi, Takashi Matsui, Gerhard Hummer, Tomoko Masaike, and Takayuki Nishizaka “F1-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements” Proc. Natl. Acad. Sci. USA 113(21): E2916-E2924, DOI: 10.1073/pnas.1524720113 (2016)
Kei-ichi Okazaki and Gerhard Hummer “Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase” Proc. Natl. Acad. Sci. USA 112(34): 10720-10725, DOI: 10.1073/pnas.1500691112 (2015)
Kei-ichi Okazaki and Gerhard Hummer “Phosphate release coupled to rotary motion of F1-ATPase” Proc. Natl. Acad. Sci. USA 110(41): 16468-16473, https://doi.org/10.1073/pnas.1305497110 (2013)
Kei-ichi Okazaki, Takato Sato, and Mitsunori Takano “Temperature-Enhanced Association of Proteins Due to Electrostatic Interaction: A Coarse-Grained Simulation of Actin–Myosin Binding” J. Am. Chem. Soc. 134(21): 8918-8925, https://doi.org/10.1021/ja301447j (2012)
Hiroo Kenzaki, Nobuyasu Koga, Naoto Hori, Ryo Kanada, Wenfei Li, Kei-ichi Okazaki, Xin-Qiu Yao, and Shoji Takada “CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work” J. Chem. Theory Compt. 7(6): 1979-1989, https://doi.org/10.1021/ct2001045 (2011)
Kei-ichi Okazaki and Shoji Takada “Structural comparison of F1-ATPase: Interplay among enzyme structures, catalysis, and rotations” Structure 19(4): 588-598, https://doi.org/10.1016/j.str.2011.01.013 (2011)
Nobuyasu Koga, Tomoshi Kameda, Kei-ichi Okazaki, and Shoji Takada "Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations" Proc. Natl. Acad. Sci. USA 106(43): 18237-18242, https://doi.org/10.1073/pnas.0904756106 (2009)
Kei-ichi Okazaki and Shoji Takada “Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms” Proc. Natl. Acad. Sci. USA 105(32): 11182-11187, https://doi.org/10.1073/pnas.0802524105 (2008)
Kei-ichi Okazaki, Nobuyasu Koga, Shoji Takada, Jose N Onuchic, and Peter G Wolynes “Multiple-basin energy landscapes for large amplitude conformational motions of proteins: Structure-based molecular dynamics simulations” Proc. Natl. Acad. Sci. USA 103(32): 11844-11849, https://doi.org/10.1073/pnas.0604375103 (2006)
