Publications

Original Papers 2023

• Okamoto K, Sako Y: Two closed conformations of CRAF require the 14-3-3 binding motifs and cysteine-rich domain to be intact in live cells. J. Mol. Biol. 435, 167989 (2023)
• Murate M, Yokoyama N, Tomishige N, Richert L, Humbert N, Pollet B, Makino A, Kono N, Mauri L, Aoki J, Sako Y, Sonnino S, Kaneko M K, Kato Y, Inamori K-i, Iokuchi J-I, Mély Y, Iwabuchi K, Kobyashi T: Cell density-dependent membrane distribution of ganglioside GM3 in melanoma cells. Cell. Mol. Life Sci. 80, 167 (2023)
• Nagamine T, Sako Y: A SLiM-dependent conformational change in baculovirus IE1 controls its focus formation ability. J. Gen. Virol. 104, doi: 10.1099/jgv.0.001910 (2023)
• Tomishige N, Nasim M B, Murate M, Pollet B, Didier P, Godet J, Richert L, Sako Y, Mély Y, Kobayashi T: HIV-1 Gag targeting to the plasma membrane reorganizes sphingomyelin and cholesterol rich lipid domains. Nat. Commn. 14, 7353 (2023)
• Ono T, Yamashita T, Kano R, Inoue M, Okada S, Kano K, Koizumi S, Iwabuchi K, Hirabayashi Y, Matsuo I, Nakashima Y, Kamiguchi H, Kohro Y, Tsuda M: GPR55 contributes to neutrophil recruitment and mechanical pain induction after spinal cord compression in mice. Brain, Behavior, and Immunity 110: 276-287, 2023
• Kano K, Ishii N, Miyagawa A, Takeda H, Hirabayashi Y, Kamiguchi H, Greimel P, Matsuo I: Protecting-group-free glycosylation of phosphatidic acid in aqueous media. Organic & Biomolecular Chemistry 21: 2138-2142, 2023
• A. Niitsu, and Y. Sugita*. “Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation”, Phys. Chem. Chem. Phys. 25: 3595-3606 (2023).
• C. Tan, A. Niitsu, and Y. Sugita*. “Highly charged proteins and their repulsive interactions antagonize biomolecular condensation”, JACS Au 3: 834-848 (2023).
• S. Ito, K. Yagi, and Y. Sugita*. “Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding”, J. Chem. Phys.158: 115101 (2023).
• J. Jung, C. Kobayashi, and Y. Sugita*. “Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer”, J. Comp. Chem. 44: 1740-1749 (2023).
• H. M. Dokainish, and Y. Sugita*. “Structural Effects of Spike Protein D614G Mutation in SARS-CoV-2”, Biophys. J. 122: 1-11 (2023).
• A. Mizutani, C. Tan, Y. Sugita, and S. Takada*. “Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study”, PLoS Comp. Biol. 19: e1011321 (2023).
• D. Ugarte, S. Takada, and Y. Sugita*. “Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers”, J. Chem. Phys. 159: 075101 (2023).
• I. Yu, T. Mori, D. Matsuoka, D. Surblys, and Y. Sugita*. “SPANA: Spatial Decomposition Analysis for Cellular-Scale Molecular Dynamics Simulations”, J. Comp. Chem. 45: 498-505 (2023).
• Aoki H, Isobe Y, Yoshida M, Kang JX, Maekawa M, *Arita M. Enzymatically-epoxidized docosahexaenoic acid, 19,20-EpDPE, suppresses hepatic crown-like structure formation and nonalcoholic steatohepatitis fibrosis through GPR120. Biochim Biophys Acta Mol Cell Biol Lipids 1868, 159275 (2023)
• Ikizawa T, Ikeda K, Arita M, Kitajima S, Soga T, *Ichijo H, *Naguro I. Mitochondria directly sense osmotic stress to trigger rapid metabolic remodeling via regulation of pyruvate dehydrogenase (PDH) phosphorylation. J Biol Chem 299, 102837 (2023)
• Iino Y, Naganuma T, *Arita M. Dysregulated ceramide metabolism in mouse progressive dermatitis resulting from constitutive activation of Jak1. J Lipid Res 64, 100329 (2023)
• *Lopez-Vicario C, Sebastian D, Casulleras M, Duran-Guell M, Flores-Costa R, Aguilar F, Lozano JJ, Zhang IW, Titos E, Kang JX, Zorzano A, Arita M, *Claria J. Essential lipid autacoids rewire mitochondrial energy efficiency in metabolic dysfunction-associated fatty liver disease. Hepatology 77, 1303-1318 (2023)
• Shiratori H, Oguchi H, Isobe Y, Han KH, Sen A, Yakebe K, Takahashi D, Fukushima M, *Arita M, *Hase K. Gut microbiota-derived lipid metabolites facilitate regulatory T cell differentiation. Sci Rep 13, 8903 (2023)
• Sugihara R, Taneike M, Murakawa T, Tamai T, Ueda H, Kitazume-Taneike R, Oka T, Akazawa Y, Nishida H, Mine K, Hioki A, Omi J, Omiya S, Aoki J, Ikeda K, Nishida K, Arita M, Yamaguchi O, *Otsu K. Lysophosphatidylserine induces necrosis in pressure overloaded male mouse hearts via G protein coupled receptor 34. Nat Commun 14, 4494 (2023)
• *Mi-ichi F, Tsugawa H, Yoshida H, *Arita M. Unique features of Entamoeba glycerophospholipid metabolism; has the Entamoeba lipid metabolism network evolved through gene loss and gain to enable parasitic life cycle adaptation? mSphere 8, e0017423 (2023)
• Takeuchi T, *Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon A, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S , *Ohno H. Gut microbiota carbohydrate metabolism contributes to insulin resistance. Nature 621, 389-395 (2023)
• Kuroha S, Katada Y, Isobe Y, Uchino H, Shishikura K, Nirasawa T, Tsubota K, Negishi K, *Kurihara T, *Arita M. Long chain acyl-CoA synthetase 6 facilitates the local distribution of di-docosahexaenoic acid- and ultra-long-chain-PUFA-containing phospholipids in the retina to support normal visual function in mice. FASEB J 37, e23151 (2023)
• Honda A, Nozumi M, Ito Y, Natsume R, Kawasaki A, Nakatsu F, Abe M, Uchino H, Matsushita N, Ikeda K, Arita M, Sakimura K, *Igarashi M. Very-long-chain fatty acids (VLCFAs) are crucial to neuronal polarity by providing sphingolipids to lipid rafts. Cell Rep 42(10), 113195 (2023)
• Tsumagari K, Isobe Y, Ishihama Y, Seita J, *Arita M, *Imami K. Application of liquid-liquid extraction for N-terminal myristoylation proteomics. Mol Cell Proteomics 22(12), 100677 (2023)
• Fujiwara K, Maekawa M, Iimori Y, Ogawa A, Urano T, Kono N, Takeda H, Higashiyama H, Arita M, *Murai J. Crucial role of single-stranded DNA binding in enhancing sensitivity to DNA-damaging agents for Schlafen 11 and Schlafen 13. iScience 26(12), 108529 (2023)
• Tachida Y#, Hirayama H#, Suzuki T: Amino acid editing of NFE2L1 by PNGase causes abnormal mobility on SDS-PAGE. Biochim. Biophys. Acta General Subjects 1867, 130494 (2023) (#= equally contributed)