Personnel Information

写真a

ISHITANI RYUICHIRO


Job title

Professor
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Campus Career 【 display / non-display 】

  • 2024.01
    -
    2024.09
    Tokyo Medical and Dental University， Medical Research Institute， Division of Biological Data Science， -， Professor
  • 2024.10
    -
    Now
    Institute of Science Tokyo， -， Institute of Integrated Research， Biological Data Science， Computational Drug Discovery and Design， Professor
  • 2024.10
    -
    Now
    Institute of Science Tokyo， -， Graduate Schools， Integrative Molecular Biomedicine， Computational Drug Discovery and Design， Professor
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Research Theme 【 display / non-display 】

  • Investigation of transposon mechanisms and their applications, 2025.04 - 2030.03

  • Development of innovative therapies targeting mitochondrial regulation by one-carbon metabolic enzyme, 2024.09 - 2027.09

  • Structural biology of membrane transporters involved in the efflux mechanism of organic molecules, 2017.04 - 2020.03

  • Elucidation of MAPK signaling pathways and biological processes based on mathematical science, 2016.06 - 2021.03

  • Molecular mechanism of membrane proteins regulated by physical stimuli, 2016.04 - 2021.03

  • Structural and functional analyses of organic acid exporters for efficient organic acid production, 2016.04 - 2019.03

  • Structural biology of multidrug transporters, 2013.04 - 2017.03

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Published Papers & Misc 【 display / non-display 】

  1. Akiba, R; Moriwaki, Y; Ishitani, R; Yoshikawa, N. Multi-objective optimization for designing structurally similar proteins with dissimilar sequences SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS-METHODS. 2026.12; 6 (1): ( DOI )

  2. Watanabe A, Kanematsu K, Hizukuri Y, Hori T, Ogiwara S, Okuno T, Saito M, Ito T, Shibuya C, Akiyama Y, Toyota S, Moriwaki Y, Yamano K, Koyano F, Kajitani T, Ishitani R, Yamashina M, Kosako H, Matsuda N. YhbO is a DJ-1 family glyoxalase and α-oxoaldehyde hydratase that confers resistance to reactive carbonyl stress (112). The Journal of biological chemistry. 2026.06; 113300. ( PubMed, DOI )

  3. Hori T, Moriwaki Y, Ishitani R. Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways. Journal of chemical theory and computation. 2026.05; 22 (10): 5259-5270. ( PubMed, DOI )

  4. Moriwaki Y, Shiraishi T, Katsuyama Y, Matsuda K, Zhang J, Ose T, Minami A, Oikawa H, Kuzuyama T, Ishitani R, Terada T. High-Throughput Prediction of Protein-Protein Interactions Uncovers Hidden Molecular Networks in Biosynthetic Gene Clusters. Computational and structural biotechnology journal. 2026; 35 (1): 0149. ( PubMed, DOI )

  5. Sano, FK; Shimizume, K; Kobayashi, K; Awazu, T; Kawakami, K; Akasaka, H; Kobayashi, TA; Tanaka, T; Okamoto, HH; Hirano, H; Kusakizako, T; Shihoya, W; Kise, Y; Itoh, Y; Ishitani, R; Okada, Y; Sako, Y; Yanagawa, M; Inoue, A; Nureki, O. Insights into G-protein coupling preference from cryo-EM structures of G<sub>q</sub>-bound PTH1R NATURE CHEMICAL BIOLOGY. 2025.12; 21 (12): 1906-1914. ( PubMed, DOI )

  6. Zhang Y, Ishitani R, Takemoto M, Tomita A. Generalizable compound protein interaction prediction with a model incorporating protein structure aware and compound property aware language model representations. Communications chemistry. 2025.12; 9 (1): 37. ( PubMed, DOI )

  7. Ishitani, R; Moriwaki, Y. Improving Stereochemical Limitations in Protein-Ligand Complex Structure Prediction ACS OMEGA. 2025.11; 10 (46): 56075-56084. ( PubMed, DOI )

  8. Watanabe, A; Ogiwara, S; Saito, M; Mishima, M; Yamashina, M; Ishitani, R; Ito, Y; Tanaka, K; Koyano, F; Yamano, K; Kosako, H; Moriwaki, Y; Matsuda, N. The reaction mechanism for glycolysis side product degradation by Parkinson's disease-linked DJ-1 JOURNAL OF CELL BIOLOGY. 2025.06; 224 (8): ( PubMed, DOI )

  9. Ishitani, R; Takemoto, M; Tomii, K. Protein ligand binding site prediction using graph transformer neural network PLOS ONE. 2024.08; 19 (8): e0308425. ( PubMed, DOI )

  10. Molecular Design Method Using a Reversible Tree Representation of Chemical Compounds and Deep Reinforcement Learning. 2022.09; 62 (17): 4032-4048. ( PubMed, DOI )

  11. Towards universal neural network potential for material discovery applicable to arbitrary combination of 45 elements. 2022.05; 13 (1): 2991. ( PubMed, DOI )

  12. Lateral access mechanism of LPA receptor probed by molecular dynamics simulation. 2022; 17 (2): e0263296. ( PubMed, DOI )

  13. Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. 2021.03; 10 ( PubMed, DOI )

  14. Structural biology of the multidrug and toxic compound extrusion superfamily transporters. 2020.12; 1862 (12): 183154. ( PubMed, DOI )

  15. Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation. 2020.05; 3 (1): 240. ( PubMed, DOI )

  16. Identification of Potent In Vivo Autotaxin Inhibitors that Bind to Both Hydrophobic Pockets and Channels in the Catalytic Domain. 2020.03; 63 (6): 3188-3204. ( PubMed, DOI )

  17. Crystal structure of Drosophila Piwi. 2020.02; 11 (1): 858. ( PubMed, DOI )

  18. Author Correction: Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. 2020.02; 578 (7794): E19. ( PubMed, DOI )

  19. Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc. 2019.06; 26 (6): 510-517. ( PubMed, DOI )

  20. Structural basis for oligomerization of the prokaryotic peptide transporter PepTSo2. 2019.05; 75 (Pt 5): 348-358. ( PubMed, DOI )

  21. Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9. 2019.04; 10 (1): 1968. ( PubMed, DOI )

  22. Crystal structure of plant vacuolar iron transporter VIT1. 2019.03; 5 (3): 308-315. ( PubMed, DOI )

  23. Structural Basis of H+-Dependent Conformational Change in a Bacterial MATE Transporter. 2019.02; 27 (2): 293-301. ( PubMed, DOI )

  24. Cap-specific terminal N 6-methylation of RNA by an RNA polymerase II-associated methyltransferase. 2019.01; 363 (6423): ( PubMed, DOI )

  25. Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex. 2018.12; 74 (Pt 12): 810-816. ( PubMed, DOI )

  26. Vibrational and Molecular Properties of Mg2+ Binding and Ion Selectivity in the Magnesium Channel MgtE. 2018.10; 122 (42): 9681-9696. ( PubMed, DOI )

  27. Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1. 2018.10; 9 (1): 4424. ( PubMed, DOI )

  28. An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin. 2018.10; 115 (7): 1281-1291. ( PubMed, DOI )

  29. Free Energy Landscape for the Entire Transport Cycle of Triose-Phosphate/Phosphate Translocator. 2018.09; 26 (9): 1284-1296. ( PubMed, DOI )

  30. Cryo-EM structures of the human volume-regulated anion channel LRRC8. 2018.09; 25 (9): 797-804. ( PubMed, DOI )

  31. Engineered CRISPR-Cas9 nuclease with expanded targeting space. 2018.09; 361 (6408): 1259-1262. ( PubMed, DOI )

  32. Functional roles of Mg2+ binding sites in ion-dependent gating of a Mg2+ channel, MgtE, revealed by solution NMR. 2018.04; 7 ( PubMed, DOI )

  33. Structural basis for xenobiotic extrusion by eukaryotic MATE transporter. 2017.11; 8 (1): 1633. ( PubMed, DOI )

  34. Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity. 2017.10; 3 (10): 825-832. ( PubMed, DOI )

  35. Structural insights into the competitive inhibition of the ATP-gated P2X receptor channel. 2017.10; 8 (1): 876. ( PubMed, DOI )

  36. Structural insights into ligand recognition by the lysophosphatidic acid receptor LPA6. 2017.08; 548 (7667): 356-360. ( PubMed, DOI )

  37. Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. 2017.08; 67 (4): 633-645. ( PubMed, DOI )

  38. Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1. 2017.07; 67 (1): 139-147. ( PubMed, DOI )

  39. ATP-dependent modulation of MgtE in Mg2+ homeostasis. 2017.07; 8 (1): 148. ( PubMed, DOI )

  40. Cyclic GMP-AMP as an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA. 2017.06; 86 541-566. ( PubMed, DOI )

  41. Structural insights into the nucleotide base specificity of P2X receptors. 2017.03; 7 45208. ( PubMed, DOI )

  42. Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems. 2017.03; 65 (6): 1109-1121. ( PubMed, DOI )

  43. Correction: Breakpoint Cluster Region-Mediated Inflammation Is Dependent on Casein Kinase II. 2017.01; 198 (2): 971. ( PubMed, DOI )

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Conference Activities & Talks 【 display / non-display 】

  1. Nakamura Ryoki, Kasuya Go, Takemoto Mizuki, Hattori Motoyuki, Ishitani Ryuichiro, Nureki Osamu. MDシミュレーションを用いたATP作動性イオンチャネルP2Xにおける競合的阻害剤TNP-ATPの作用機序の解明(MD simulation of ATP-gated P2X receptors reveals the inhibitory mechanism of a competitive antagonist TNP-ATP). 生物物理 2017.08.01

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Works 【 display / non-display 】

  • CueMol: Molecular Visualization Framework，Software，2000.01 - Now

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