Publications 2022

D. Matsubara, K. Kasahara, H. M. Dokainish, H. Oshima, and Y. Sugita, “Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions”, Molecules, 27, 5726 (2022)
M. Oide and Y. Sugita, “Protein Folding Intermediates on the Dimensionality Reduced Landscape with UMAP and Native Contact Likelihood”, J. Chem. Phys., 157, 075101 (2022)
H. Oshima and Y. Sugita, “Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions”, J. Chem. Inf. Model., 62, 2846-2856 (2022)
L. Heo, Y. Sugita, and M. Feig, “Protein assembly and crowding simulations”, Curr. Opin. Struct. Biol., 73, 102340 (2022)
H. Yamazaki, M. Takagi, H. Kosako, T. Hirano, and S. H. Yoshimura, “Cell Cycle-specific Phase Separation Regulated by Protein Charge Blockiness”, Nat. Cell Biol., 24, 625-632 (2022)
Y. Kimura#, H. Saito#, T. Osaki, Y. Ikegami, T. Wakigawa, Y. Ikeuchi, and S. Iwasaki, “Mito-FUNCAT-FACS Reveals Cellular Heterogeneity in Mitochondrial Translation”, RNA, 28, 895-904 (2022) (#: equal contribution)
A. Apostolopoulos and S. Iwasaki, “Into the Matrix: Current Methods for Mitochondrial Translation Studies”, J. Biochem., 171(4), 379-387 (2022)
H. M Dokainish, S. Re, T. Mori, C. Kobayashi, J. Jung, and Y. Sugita, “The Inherent Flexibility of Receptor Binding Domains in SARS-CoV-2 Spike Protein”, eLife, 11, e75720 (2022)
E. Okubo-Kurihara, A. Ali, M. Hiramoto, Y. Kurihara, Y. Abouleila, E. M. Abdelazem, T. Kawai, Y. Makita, M. Kawashima, T. Esaki, H. Shimada, T. Mori, M. Y. Hirai, T. Higaki, S. Hasezawa, Y. Shimizu, T. Masujima, and M. Matsui, “Tracking Metabolites at Single-cell Resolution Reveals Metabolic Dynamics During Plant Mitosis”, Plant Physiol., kiac093, 1-6 (2022)
T. Imaizumi, N. Umeki, R. Yoshizawa, T. Obuchi, Y. Sako, and Y. Kabashima, “Assessing Transfer Entropy from Biochemical Data”, Phys. Rev. E, 105(3), 034403 (2022)
Y. Mishima, P. Han, K. Ishibashi, S. Kimura, and S. Iwasaki, “Ribosome Slowdown Triggers Codon-mediated mRNA Decay Independently of Ribosome Quality Control”, EMBO J., 41(5), e109256 (2022)
T. Fujita, T. Yokoyama, M. Shirouzu, H. Taguchi, T. Ito, and S. Iwasaki, “The Landscape of Translational Stall Sites in Bacteria Revealed by Monosome and Disome Profiling”, RNA, 28(3), 290-302 (2022)
S. Mise, A. Matsumoto, K. Shimada, T. Hosaka, M. Takahashi, K. Ichihara, H. Shimizu, C. Shiraishi, D. Saito, M. Suyama, T. Yasuda, T. Ide, Y. Izumi, T. Bamba, T. Kimura-Someya, M. Shirouzu, H. Miyata, M. Ikawa, and K. I. Nakayama, “Kastor and Polluks Polypeptides Encoded by a Single Gene Locus Cooperatively Regulate VDAC and Spermatogenesis”, Nat. Commun., 13, 1071 (2022)
J. K. Chhipi-Shrestha, T. Schneider-Poetsch, T. Suzuki, M. Mito, K. Khan, N. Dohmae, S. Iwasaki*, and M. Yoshida *, “Splicing Modulators Elicit Global Translational Repression by Condensate-prone Proteins Translated from Introns”, Cell Chem. Biol., 29(2), 259-275.e10 (2022)
Y. Nakagawa, H. C.-H. Shen, Y. Komi, S. Sugiyama, T. Kurinomaru, Y. Tomabechi, E. Krayukhina, K. Okamoto, T. Yokoyama, M. Shirouzu, S. Uchiyama, M. Inaba, T. Niwa, Y. Sako, H. Taguchi, and M. Tanaka, “Amyloid Conformation-dependent Disaggregation in a Reconstituted Yeast Prion System”, Nat. Chem. Biol., 18, 321–331 (2022)
K. K. Hui, R. Endo, A. Sawa, and M. Tanaka, “A Perspective on the Potential Involvement of Impaired Proteostasis in Neuropsychiatric Disorders” Biol. Psychiatry, 91(4), 335-345 (2022)
T. Okada, H. Miyagi, Y. Sako, M. Hiroshima, and A. Mochizuki, “Origin of Diverse Phosphorylation Patterns in the ERBB System”, Biophys. J., 121(3), 470-480 (2022)
K. Yagi, S. Re, T. Mori, and Y. Sugita, “Weight Average Approaches for Predicting Dynamical Properties of Biomolecules”, Curr. Opin. Struct. Biol., 72, 88-94 (2022)
W. Heo, K. Hasegawa, K. Okamoto, Y. Sako, K. Ishii, and T. Tahara, “Scanning Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy: Conformational Dynamics of DNA Holliday Junction from Microsecond to Subsecond”, J. Phys. Chem. Lett., 13(5), 1249-1257 (2022)
K. Kawakami*, M. Yanagawa*, S. Hiratsuka, M. Yoshida, Y. Ono, M. Hiroshima, M. Ueda, J. Aoki, Y. Sako**, and A. Inoue**, “Heterotrimeric Gq Proteins Act as a Switch for GRK5/6 Selectivity Underlying β-arrestin Transducer Bias”, Nat. Commun., 13, 487 (2022) (*: Co-first author, **: Co-correspondence)
Q. Wu, Y. Shichino, T. Abe, T. Suetsugu, A. Omori, H. Kiyonari, S. Iwasaki, and F. Matsuzaki, “Selective Translation of Epigenetic Modifiers Affects the Temporal Pattern and Differentiation of Neural Stem Cells”, Nat. Commun., 13, 470 (2022)
K. Kinoshita, Y. Tsubota, S. Tane, Y. Aizawa, R. Sakata, K. Takeuchi, K. Shintomi, T. Nishiyama, and T. Hirano, “A Loop Extrusion–independent Mechanism Contributes to Condensin I–mediated Chromosome Shaping”, J. Cell Biol., 221(3), e202109016 (2022)

Publications 2021

S. Sekine, T. Uejima, and H. Ehara, “RNA Polymerase-associated Transcription Elongation Factors”, RNA Polymerases as Molecular Motors 2nd Edition, Chapter 4, eds. R. Landick, T. Strick, and J. Wang, Royal Society of Chemistry (2021)
H. Yagi, T. Kasai, E. Rioual, T. Ikeya, and T. Kigawa, “Molecular Mechanism of Glycolytic Flux Control Intrinsic to Human Phosphoglycerate Kinase”, Proc. Natl. Acad. Sci. U.S.A., 118(50), e2112986118 (2021)
K. Kashiwagi#, Y. Shichino#, T. Osaki#, A. Sakamoto, M. Nishimoto, M. Takahashi, M. Mito, F. Weber, Y. Ikeuchi*, S. Iwasaki*, and T. Ito*, “eIF2B-capturing Viral Protein NSs Suppresses the Integrated Stress Response”, Nat. Commun., 12, 7102. (2021) (#: equal contribution)
M. Kukimoto-Niino, K. Ihara, K. Murayama, and M. Shirouzu, “Structural Insights into the Small GTPase Specificity of the DOCK Guanine Nucleotide Exchange Factors”, Curr. Opin. Struct. Biol., 71, 249-258 (2021)
R. Nussinov, and M. Shirouzu,”Editorial Overview: Catalysis and Regulation: The Beating Heart of Biology” Curr. Opin. Struct. Biol., 71, iii-v (2021)
Y. Chadani, N. Sugata, T. Niwa, Y. Ito, S. Iwasaki, and H. Taguchi, “Nascent Polypeptide within the Exit Tunnel Stabilizes the Ribosome to Counteract Risky Translation”, EMBO J., 40(23), e108299 (2021)
M. Abe, A. Makino, M. Murate, F. Hullin-Matsuda, M. Yanagawa, Y. Sako, and T. Kobayashi, “PMP2/FABP8 Induces PI(4,5)P2-dependent Transbilayer Reorganization of Sphingomyelin in the Plasma Membrane”, Cell Rep., 37(6), 109935 (2021)
M. Akiyama, R. Ueki, M. Yanagawa, M. Abe, M. Hiroshima, Y. Sako, and S. Sando, “DNA-based Synthetic Growth Factor Surrogates with Fine-tuned Agonism”, Angew. Chem. Int. Ed., 60(42), 22745-22752 (2021)
C. Kobayashi, Y. Matsunaga, J. Jung, and Y. Sugita, “Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase”, Proc. Natl. Acad. Sci. U.S.A., 118(40), e2105507118 (2021)
K. Fujiyama, N. Kato, S. Re, K. Kinugasa, K. Watanabe, R. Takita, T. Nogawa, T. Hino, H. Osada, Y. Sugita, S. Takahashi, and S. Nagano, “Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons”, Angew. Chem. Int. Ed., 60(41), 22401-22410 (2021)
R. Yoshizawa, N. Umeki, A. Yamamoto, M. Okada, M. Murata, and Y. Sako, “p52Shc Regulates the Sustainability of ERK Activation in a RAF-independent Manner”, Mol. Biol. Cell, 32(19), 1838-1848 (2021)
Y. Kuwashima, M. Yanagawa, M. Abe, M. Hiroshima, M. Ueda, M. Arita, and Y. Sako, “Comparative Analysis of Single-Molecule Dynamics of TRPV1 and TRPV4 Channels in Living Cells”, Int. J. Mol. Sci., 22(16), 8473 (2021)
K. Ichihara, A. Matsumoto, H. Nishida, Y. Kito, H. Shimizu, Y. Shichino, S. Iwasaki, K. Imami, Y. Ishihama, and K. I. Nakayama, “Combinatorial Analysis of Translation Dynamics Reveals eIF2 Dependence of Translation Initiation at Near-cognate Codons”, Nucleic Acids Res., 49(13), 7298-7317 (2021)
M. Kukimoto-Niino, K. Katsura, R. Kaushik, H. Ehara, T. Yokoyama, T. Uchikubo-Kamo, R. Nakagawa, C. Mishima-Tsumagari, M. Yonemochi, M. Ikeda, K. Hanada, K. Y. J. Zhang, and M. Shirouzu, “Cryo-EM Structure of the Human ELMO1-DOCK5-Rac1 Complex”, Sci. Adv., 7(30), eabg3147 (2021)
J. Jung, K. Kasahara, C. Kobayashi, H. Oshima, T. Mori, and Y. Sugita, “Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems”, J. Chem. Theory Comput., 17(8), 5312-5321 (2021)
K. Kasahara, S. Re, G. Nawrocki, H. Oshima, C. Mishima-Tsumagari, Y. Miyata-Yabuki, M. Kukimoto-Niino, I. Yu, M. Shirouzu, M. Feig, and Y. Sugita, “Reduced Efficacy of a Src Kinase Inhibitor in Crowded Protein Solution”, Nat. Commun., 12, 4099 (2021)
H.-O. Iwakawa, A. Y.W. Lam, A. Mine, T. Fujita, K. Kiyokawa, M. Yoshikawa, A. Takeda, S. Iwasaki, and Y. Tomari, “Ribosome Stalling Caused by the Argonaute-microRNA-SGS3 Complex Regulates the Production of Secondary siRNAs in Plants”, Cell Rep., 35(13), 109300 (2021)
T. Mori, G. Terashi, D. Matsuoka, D. Kihara, and Y. Sugita, “Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps”, J. Chem. Inf. Model., 61(7), 3516–3528 (2021)
L. Bracun, A. Yamagata, B. M. Christianson, T. Terada, D. P. Canniffe, M. Shirouzu, and L.N. Liu, “Cryo-EM Structure of the Photosynthetic RC-LH1-PufX Supercomplex at 2.8-Å Resolution”, Sci. Adv., 7(25), eabf8864 (2021)
K. Shintomi and T. Hirano, “Guiding Functions of the C-terminal Domain of Topoisomerase IIα Advance Mitotic Chromosome Assembly”, Nat. Commun., 12, 2917 (2021)
A. Shinobu, C. Kobayashi, Y. Matsunaga, and Y. Sugita, “Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins”, J. Chem. Inf. Model., 61(5), 2427–2443 (2021)
K. Yagi, S. Ito, and Y. Sugita, “Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations”, J. Phys. Chem. B, 125(18), 4701-4713 (2021)
Y. Mii, K. Nakazato, C.-G. Pack, T. Ikeda, Y. Sako, A. Mochizuki, M. Taira, and S. Takada, “Quantitative Analyses Reveal Extracellular Dynamics of Wnt Ligands in Xenopus Embryos”, eLife, 10, e55108 (2021)
S. Makino, T. Kawamata, S. Iwasaki*, and Y. Ohsumi*, “Selectivity of mRNA Degradation by Autophagy in Yeast”, Nat. Commun., 12, 2316 (2021)
M. Hiroshima and Y. Sako, “In-Cell Single-Molecule Analysis of Molecular State and Reaction Kinetics Coupling”, Advances in Experimental Medicine and Biology, 1310, 59-80. J. K. Kim, J. K. Kim, C.-G. Pack eds. Springer (2021)
Y. Nagayoshi, T. Chujo, S. Hirata, H. Nakatsuka, C.-W. Chen, M. Takakura, K. Miyauchi, Y. Ikeuchi, B. C. Carlyle, R. R. Kitchen, T. Suzuki, F. Katsuoka, M. Yamamoto, Y. Goto, M. Tanaka, K. Natsume, A. C. Nairn, T. Suzuki, K. Tomizawa, and F.-Y. Wei, “Loss of Ftsj1 Perturbs Codon-specific Translation Efficiency in the Brain and is Associated with X-linked Intellectual Disability”, Sci. Adv., 7(13), eabf3072 (2021)