Publications

Original Papers 2022

• Hung H, Nagatsuka Y, Soldà T, Kodali VK, Iwabuchi K, Kamiguchi H, Kano K, Matsuo I, Ikeda K, Kaufman RJ, Molinari M, Greimel P, Hirabayashi Y: Selective involvement of UGGT variant: UGGT2 in protecting mouse embryonic fibroblasts from saturated lipid-induced ER stress. Proceedings of the National Academy of Sciences USA 119: e2214957119, 2022
• C. Tan, J. Jung, C. Kobayashi, D. Ugarte, S. Takada, and Y. Sugita*. “Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations”, PLoS Comp. Biol. 18: e1009578 (2022).
• S. Ito, K. Yagi, and Y. Sugita*. “Computational analysis on the allostery of tryptophan synthase: relationship between α/β-ligand binding and distal domain closure”, J. Phys. Chem. B 126: 3300-3308 (2022).
• A. Shinobu, S. Re, and Y. Sugita*. “Practical Protocols for efficient sampling of kinase-inhibitor binding pathways using two-dimensional replica-exchange molecular dynamics”, Front. Mol. Biosci. 9: 878830 (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).
• 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).
• D. Matsubara, K. Kasahara, H. 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).
• Y. Zhang, C. Kobayashi, X. Cai, S. Watanabe, A. Tsutsumi, M. Kikkawa, Y. Sugita, and K. Inaba*. “Multiple sub state structures of SERCA2b reveal conformational overlap at transition steps during the catalytic cycle”, Cell reports 41: 111760 (2022).
• Y. Matsunaga, M. Kamiya, H. Oshima, J. Jung, S. Ito, and Y. Sugita*. “Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation”, Biophys. Rev.14: 1-10 (2022).
• Mori K, Kuroha S, Hou J, Jeong H, Ogawa M, Ikeda S, Kang JX, Negishi K, Torii H, *Arita M, *Kurihara T, Tsubota K. Lipidomic analysis revealed n-3 polyunsaturated fatty acids suppressed choroidal thinning and myopia progression in mice. FASEB J 36, e22312 (2022)
• Morimoto K, Fukuda K, Ito Y, Tahara U, Sasaki T, Shiohama A, Kawasaki H, Kawakami E, Naganuma T, Arita M, Sasaki H, Koseki H, Matsui T, *Amagai M. Microbiota-independent spontaneous dermatitis associated with increased sebaceous lipid production in Tmem79-deficient mice. J Invest Dermatol 142, 2864-2872 (2022)
• Mi-ichi F, Tsugawa H, Arita M, Yoshida H. Pleiotropic roles of cholesteryl sulfate during Entamoeba encystation; involvement in cell rounding and development of membrane impermeability. mSphere 7, e0029922 (2022)
• McDonald JG, Ejsing CS, Kopczynski D, Holcapek M, Aoki J, Arita M, Arita M, Baker ES, Bertrand-Michel J, Bowden JA, Brugger B, Ellis SR, Fedorova M, Griffiths WJ, Han X, Hartler J, Hoffmann N, Koelmel JP, Kofeler HC, Mitchell TW, O’Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Ulmer CZ, Wenk MR, Witting M, Wolrab D, Xia Y, *Ahrends R, *Liebisch G, *Ekroos K. Introducing the lipidomics minimal reporting checklist. Nat Metab 4, 1086-1088 (2022)
• Yoshida M, Ishihara T, Isobe Y, *Arita M. Genetic deletion of Cyp4f18 disrupts the omega-3 epoxidation pathway and results in psoriasis-like dermatitis. FASEB J 36, e22648 (2022)
• Uchino H, *Tsugawa H, Takahashi H, *Arita M. Computational mass spectrometry accelerates C=C position-resolved untargeted lipidomics using oxygen attachment dissociation. Commun Chem 5, 162 (2022) selected in 2022 Editor’s Highlights
• Ariyasu Y, Sato Y, Isobe Y, Taniguchi K, *Yanagita M, *Arita M. Sterol O-acyltransferase inhibition ameliorates high-fat diet-induced renal fibrosis and tertiary lymphoid tissue maturation after ischemic reperfusion injury. Int J Mol Sci 23, 15465 (2022)
• Takahashi T, Uchibayashi T, Ishii N, Matsuo I, Yoshida Y, Suzuki T: Luminescence detection of peptide:N-glycanase activity using engineered split inteins. Chem. Commun. 58, 13282-13285 (2022)
• Huang S#, Haga Y#, Li J#, Zhang J, Kweon HK, Seino J, Hirayama H, Fujita M, Moremen KW, Andrews P, Suzuki T, Wang Y: Mitotic phosphorylation inactivates the Golgi mannosidase MAN1A1. Cell Rep 41, 111679 (2022) (#: equally contributed)
• Huang C, Seino J, Fujihira H, Sato K, Fujinawa R, Sumer-Bayraktar Z, Ishii N, Matsuo I, Nakaya S, Suzuki T: Occurrence of free N-glycans with a single GlcNAc at the reducing termini in animal sera. Glycobiology 32, 314-332 (2022)
• Hirayama H, Tachida Y, Seino J, Suzuki T: A method for assaying peptide:N-glycanase/N-Glycanase 1 activities in crude extracts using an N-glycosylated cyclopeptide. Glycobiology 32, 110-122 (2022)
• Kawakami K, Yanagawa M, Hiratsuka S, Yoshida M, Ono Y, Hiroshima M, Ueda M, Aoki J, Sako Y, Inoue A: The origin of b-arrestin transducer bias: heterotrimeric Gq as a switch for GRK5/6 selectivity. Nat. Comm. 13, 487 (2022)
• Okada T, Miyagi H, Sako Y, Hiroshima M, Mochizuki A: Origin of diverse phosphorylation patterns in the ERBB system. Biophys. J. 121, 470-480 (2022)
• Nakagawa Y, Shen H C-H, Komi Y, Sugiyama S, Kurinomaru T, Tomabechi Y, Krayukhina E, Okamoto K, Yokoyama T, Shirouzu M, Uchiyama S, Inaba M, Niwa T, Sako Y, Taguchi H, Tanaka M: Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system. Nat. Chem. Biol. 18, 321-331 (2022)
• Keo W, Hasegawa K, Okamoto K, Sako Y, Ishii K, Tahara T: Scanning two-dimensional fluorescence lifetime correlation spectroscopy: Conformational dynamics of DNA Hollyday-junction from microsecond to sub-second. Phys. Chem, Lett. 13, 1249-1257 (2022)
• Imaizumi T, Umeki N, Yoshizawa R, Obuchi T, Sako Y, Kabashima Y: Assessing transfer entropy from biochemical data. Phys. Rev. E. 105, 034403 (1-13) (2022)
• Yamaji-Hasegawa A, Murate M, Inaba T, Dohmae N, Sato M, Fujimori F, Sako Y, Grimel P, Kobayashi T: A novel sterol binding protein reveals heterogeneous cholesterol distribution in neurite outgrowth and in late endosome/lysosomes. Cell. Mol. Life Sci. 79, 324 (1-19) (2022)
• Arata Y, Shiga I, Ikeda Y, Jurica P, Kimura H, Kiyono K, Sako Y: Insulin signaling shapes fractal scaling of C. elegans behavior. Sci. Rep. 12, 10481 (1-10) (2022)
• Wibisana J N, Inaba T, Shinohara H, Yumoto N, Hayashi T, Umeda M, Ebisawa M, Nikaido I, Sako Y, Okada M: Enhanced transcriptional heterogeneity mediated by NF-kB super-enhancers. PLoS Genetics, 18, e1010235 (1-25) (2022)
• Maeda R, Tamakgaki-Asahina H, Sato T, Yanagawa M, Sako Y: Threonine phosphorylation regulates the molecular assembly and signaling of EGFR in cooperation with membrane lipids. J. Cell Sci. 135, jcs260355 (1-12) (2022)