List of publications :

JAIST研究者総覧

Year : 2024 2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 -2010

  • 2024

    • Chythra J N, O. Guvench, A. D. MacKerell Jr, T. Yamaguchi, S. S. Mallajosyula
      Refinement of the drude polarizable force field for hexose monosaccharides: Capturing ring conformational dynamics with enhanced accuracy
      J. Chem. Theory Comput., 20, 9161–9177, 2024

  • 2023

    • S. Seetaha, N. Kamonsutthipaijit, M. Yagi‑Utsumi, Y. Seako, T. Yamaguchi, S. Hannongbua, K. Kato, K. Choowongkomon
      Biophysical characterization of p51 and p66 monomers of HIV-1 reverse transcriptase with their inhibitors
      Protein J., 42, 741–752, 2023

    • H. Tatsuoka, T. Yamaguchi
      NMR analyses of carbohydrate–water and water–water interactions in water/DMSO mixed solvents, highlighting various hydration behaviors of monosaccharides glucose, galactose and mannose
      Bull. Chem. Soc. Jpn., 96, 168-174, 2023

    総合論文、図書

    • 山口拓実, 谷中冴子, 加藤晃一
      分子シミュレーションによる糖鎖の3次元構造の動態予測
      タンパク質の構造解析手法とIn silicoスクリーニングへの応用事例, 技術情報協会, pp.237-245, 2023

  • 2022

    • S. Horiuchi, T. Yamaguchi, J. Tessarolo, H. Tanaka, E. Sakuda, Y. Arikawa, E. Meggers, G. H. Clever, K. Umakoshi
      Symmetry-Breaking Host–guest Assembly in a Hydrogen-bonded Supramolecular System
      Nature Commun., 14, 155, 2023

    総合論文、図書

    • K. Kato, T. Yamaguchi, M. Yagi-Utsumi
      Experimental and computational characterization of dynamic biomolecular interaction systems involving glycolipid glycans
      Glycoconj. J. 39, 219–228, 2022

  • 2021

    • S. Ohno, N. Manabe, T. Yamaguchi, J. Uzawa, Y. Yamaguchi
      Ribitol in solution is an equilibrium of asymmetric conformations
      Molecules, 26, 5471, 2021

    • T. Watanabe, H. Yagi, S. Yanaka, T. Yamaguchi, K. Kato
      Comprehensive characterization of oligosaccharide conformational ensembles with conformer classification by free-energy landscape via reproductive kernel Hilbert space
      Phys. Chem. Chem. Phys., 23, 9753–9760, 2021

  • 2020

    • K. Yamada, T. Yamaguchi, R. Ohashi, S. Ohki, K. Deguchi, K. Hashi, A. Goto, T. Shimizu
      Field-stepwise-swept QCPMG solid-state 115In NMR of indium oxide
      Solid State Nuclear Magnetic Resonance, 109, 101688, 2020

    • K. Yamada, Y. Yamaguchi, Y. Uekusa, K. Aoki, I. Shimada, T. Yamaguchi, K. Kato
      Solid-state 17O NMR analysis of synthetically 17O-enriched D-glucosamine
      Chem. Phys. Lett., 749, 137455, 2020

    総合論文、図書

    • T. Yamaguchi
      Delineating the dynamic conformations of oligosaccharides by combining molecular simulation and NMR spectroscopy
      Trends Glycosci. Glycotechnol. 32, E93–E98 (J79-J84, Japanese edition), 2020

    • 加藤晃一, 山口拓実
      糖鎖の動的構造解析
      糖鎖生物学（北島 健, 佐藤ちひろ, 門松健治, 加藤晃一編）, 名古屋大学出版会, pp.109-110, 2020

  • 2019

    • T. Suzuki, S. Yanaka, T. Watanabe, G. Yan, T. Satoh, H. Yagi, T. Yamaguchi, K. Kato
      Remodeling of the oligosaccharide conformational space in the prebound state to improve lectin-binding affinity
      Biochemistry, 34, 3180–3185, 2020

    • S. Yanaka, R. Yogo, R. Inoue, M. Sugiyama, S. G. Itoh, H. Okumura, Y. Miyanoiri, H. Yagi, T. Satoh, T. Yamaguchi, K. Kato
      Dynamic views of the Fc region of immunoglobulin G provided by experimental and computational observations
      Antibodies, 8, 39, 2019

    総合論文、図書

    • 山口拓実
      常磁性効果を活用した糖鎖の動的立体構造解析
      日本核磁気共鳴学会機関誌, 10, 42-47, 2019

    • 加藤晃一, 山口拓実, 矢木真穂
      糖鎖解析技術：核磁気共鳴（NMR）法
      糖質分析（日本分析化学会編）, 丸善出版, pp.246-252, 2019

    • 矢木宏和, 鈴木達哉, 谷中冴子, 山口拓実, 加藤晃一
      核磁気共鳴分光法と分子動力学計算を通じて観る糖鎖の動的構造とレクチンの糖鎖認識の理解
      医学のあゆみ, 269, 761-767, 2019

  • 2018

    • H. Yagi, G. Yan, T. Suzuki, S. Tsuge, T. Yamaguchi, K. Kato
      Lewis X-carrying neoglycolipids evoke selective apoptosis in neural stem cells
      Neurochem. Res. 43, 212-218, 2018

    総合論文、図書

    • T. Yamaguchi and K. Kato
      Molecular dynamics of gangliosides
      Methods Mol. Biol. 1804, 411-417, 2018

    • 山口拓実, 渡邉東紀男, 矢木宏和, 加藤晃一
      分子動力学計算とNMR計測を用いた糖鎖の配座空間探査
      J. Comput. Chem. Jpn. 17, 1-7, 2018

    • K. Kurihara, M. Matsuoc, T. Yamaguchi, S. Sato
      Synthetic approach to biomolecular science by cyborg supramolecular chemistry
      BBA - General Subjects, 1862, 358-364, 2018

  • 2017

    • Y. Sakae, T. Satoh, H. Yagi, S. Yanaka, T. Yamaguchi, Y. Isoda, S. Iida, Y. Okamoto, K. Kato
      Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa
      Sci. Rep. 7, 13780, 2017

    • G. Yan, T. Yamaguchi, T. Suzuki, S. Yanaka, S. Sato, M. Fujita, K. Kato
      Hyper-assembly of self-assembled glycoclusters mediated by specific carbohydrate–carbohydrate interactions
      Chem. Asian J. 12, 968-972, 2017

    • T. Suzuki, M. Kajino，S. Yanaka，T. Zhu，H. Yagi，T. Satoh，T. Yamaguchi，K. Kato
      Conformational analysis of a high-mannose-type oligosaccharide displaying glucosyl determinant recognised by molecular chaperones using NMR-validated molecular dynamics simulation
      ChemBioChem, 18, 396-410, 2017

    総合論文、図書

    • K. Kato, H. Yagi, T. Yamaguchi
      NMR characterization of the dynamic conformations of oligosaccharides
      In: Modern Magnetic Resonance (G. Webb eds), Springer, 2017, https://doi.org/10.1007/978-3-319-28275-6_35-1

    • M. Yagi-Utsumi, T. Yamaguchi, Y. Uekusa, K. Kato
      NMR characterization of the conformations, dynamics, and interactions of glycosphingolipids
      In: NMR in Glycoscience and Glycotechnology (K. Kato and T. Peters eds), RSC Publishing, pp161-178, 2017

  • 2016

    • T. Satoh, T. Toshimori, G. Yan, T. Yamaguchi, K. Kato
      Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control
      Sci. Rep. 6, 20575, 2016

    • S. Seetaha, M. Yagi-Utsumi, T. Yamaguchi, K. Ishii, S. Hannongbua, K. Choowongkomon, K. Kato
      Application of site-specific spin labeling for NMR detecting inhibitor-induced conformational change of HIV-1 reverse transcriptase
      ChemMedChem, 11, 363-366, 2016

    総合論文、図書

    • M. Yagi-Utsumi, T. Yamaguchi, R. Kitahara, K. Kato
      NMR explorations of biomolecular systems with rapid conformational exchanges
      In: Molecular Science of Fluctuations toward Biological Functions (M. Terazima, M. Kataoka, R. Ueoka, and Y. Okamoto eds), Springer, pp87-103, 2016

  • 2015

    • T. Zhu, T. Yamaguchi, T. Satoh, K. Kato
      A hybrid strategy for the preparation of 13C-labeled high-mannose-type oligosaccharides with terminal glucosylation for NMR study
      Chem. Lett. 44, 1744-1746, 2015

    • R. Thammaporn, M. Yagi-Utsumi, T. Yamaguchi, P. Boonsri, P Saparpakorn, K. Choowongkomon, S. Techasakul, K. Kato, S. Hannongbua
      NMR characterization of HIV-1 reverse transcriptase binding to various non-nucleoside reverse transcriptase inhibitors with different activities
      Sci. Rep. 5, 15806, 2015

    • S. Sato, Y. Yoshimasa, D. Fujita, M. Yagi-Utsumi, T. Yamaguchi, K. Kato, M. Fujita
      A self-assembled spherical complex displaying a gangliosidic glycan cluster capable of interacting with amyloidogenic proteins
      Angew. Chem. Int. Ed. 54, 8435-8439, 2015

    • H. Yagi, Y. Zhang, M. Yagi-Utsumi, T. Yamaguchi, S. Iida, Y. Yamaguchi, K. Kato
      Backbone 1H, 13C, and 15N resonance assignments of the Fc fragment of human immunoglobulin G glycoprotein
      Biomol. NMR Assign. 9, 257-260, 2015

    • H. Yagi, M. Nakamura, J. Yokoyama, Y. Zhang, T. Yamaguchi, S. Kondo, J. Kobayashi, T. Kato, E. Y. Park, S. Nakazawa, N. Hashii, N. Kawasaki, K. Kato
      Stable isotope labeling of glycoprotein expressed in silkworms using immunoglobulin G as a test molecule
      J. Biomol. NMR, 62, 157-167, 2015

    • H. Yagi, N. Fukuzawa, Y. Tasaka, K. Matsuo, Y. Zhang, T. Yamaguchi, S. Kondo, S. Nakazawa, N. Hashii, N. Kawasaki, T. Matsumura, K. Kato
      NMR-based structural validation of therapeutic antibody produced in Nicotiana benthamiana
      Plant Cell Rep. 34, 959-968, 2015

    • S. Sato, R. Takeuchi, M. Yagi-Utsumi, T. Yamaguchi, Y. Yamaguchi, K. Kato, M. Fujita
      A self-assembled, π-stacked complex as a finely-tunable magnetic aligner for biomolecular NMR applications
      Chem. Commun. 51, 2540-2543, 2015

    • Y. Zhang, T. Yamaguchi, T. Satoh, M. Yagi-Utsumi, Y. Kamiya, Y. Sakae, Y. Okamoto, K. Kato
      Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation
      Adv. Exp. Med. Biol. 842, 217, 2015

    総合論文、図書

    • K. Kato and T. Yamaguchi
      Paramagnetic NMR probes for characterization of the dynamic conformations and interactions of oligosaccharides
      Glycoconj. J. 32, 505, 2015

    • T. Satoh, T. Yamaguchi, K. Kato
      Emerging structural insights into glycoprotein quality control coupled with N-glycan processing in the endoplasmic reticulum
      Molecules, 20, 2475, 2015

    • 山口拓実, 加藤晃一
      糖鎖の立体構造を描き出す
      生物物理, 55, 81-83, 2015

    • 山口拓実, 加藤晃一
      NMR
      糖鎖の新機能開発・応用ハンドブック, エヌ・ティー・エス, pp.265-271, 2015

    • T. Yamaguchi and K. Kato
      Paramagnetism-assisted nuclear magnetic resonance analysis of dynamic conformations and interactions of oligosaccharides
      Glycoscience: Biology and Medicine, Springer, Vol.1, pp.137-145, 2015

  • 2014

    • T. Yamaguchi, Y. Sakae, Y. Zhang, S. Yamamoto, Y. Okamoto, K. Kato
      Exploration of conformational spaces of high-mannose-type oligosaccharides by an NMR-validated simulation
      Angew. Chem. Int. Ed. 53, 10941-10944, 2014

    • T. Doi, M. Yoshida, K. Ohsawa, K. Shin-ya, M. Takagi, Y. Uekusa, T. Yamaguchi, K. Kato, T. Hirokawa, T. Natsume
      Total Synthesis and Characterization of Thielocin B1 as a Protein–Protein Interaction Inhibitor of PAC3 Homodimer
      Chem. Sci. 5, 1860-1868, 2014

    • T. Satoh, K. Suzuki, T. Yamaguchi, K. Kato
      Structural basis for disparate sugar-binding specificities in the homologous cargo receptors ERGIC-53 and VIP36
      PLoS ONE, 9, e87963, 2014

    • M. Sugiyama, H. Yagi, T. Yamaguchi, K. Kumoi, M. Hirai, Y. Oba, N. Sato, L. Porcar, A. Martel, K. Kato
      Conformational characterization of a protein complex involving intrinsically disordered protein by small-angle neutron scattering using the inverse contrast matching method: a case study of interaction between α-synuclein and PbaB tetramer as a model chaperone
      J. Appl. Crystallography , 47, 430-435, 2014

    総合論文、図書

    • Y. Yamaguchi, T. Yamaguchi, K. Kato
      Structural analysis of oligosaccharides and glycoconjugates using NMR
      In: Glycobiology of the Nervous System, Advances in Neurobiology (R.K. Yu and C.-L. Schengrund eds), Springer, pp.165-183, 2014

  • 2013

    • T. Yamaguchi, Y. Kamiya, Y.-M. Choo, S. Yamamoto, K. Kato
      Terminal spin labeling of a high-mannose-type oligosaccharide for quantitative NMR analysis of its dynamic conformation
      Chem. Lett. 42, 544-546, 2013

    • Y. Kamiya, K. Yanagi, T. Kitajima, T. Yamaguchi, Y. Chiba, K. Kato
      Application of metabolic 13C labeling in conjunction with high-field nuclear magnetic resonance spectroscopy for comparative conformational analysis of high mannose-type oligosaccharides
      Biomolecules, 3, 108-123, 2013

    • T. Yamaguchi, T. Uno, Y. Uekusa, M. Yagi-Utsumi, K. Kato
      Ganglioside-embedding small bicelles for probing membrane-landing processes of intrinsically disordered proteins
      Chem. Commun. 49, 1235-1237, 2013

    総合論文、図書

    • Y. Zhang, T. Yamaguchi, K. Kato
      New NMR tools for characterizing the dynamic conformations and interactions of oligosaccharides
      Chem. Lett. 42, 1455-1462, 2013

  • 2012

    • Y. Zhang, S. Yamamoto, T. Yamaguchi, K. Kato
      Application of paramagnetic NMR-validated molecular dynamics simulation to the analysis of a conformational ensemble of a branched oligosaccharide
      Molecules, 17, 6658-6671, 2012

    • S. Yamamoto, Y. Zhang, T. Yamaguchi, T. Kameda, K. Kato
      Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations
      Chem. Commun. 48, 4752-4754, 2012

  • 2011

    • S. Yamamoto, T. Yamaguchi, M. Erdélyi, C. Griesinger, K. Kato
      Paramagnetic lanthanide tagging for NMR conformational analyses of N-linked oligosaccharides
      Chem. Euro. J. 17, 9280–9282, 2011

  • -2010

    • M. Jang, T. Yamaguchi, K. Ohara, M. Kawano, M. Fujita
      Fluorous pores in coordination networks
      Chem. Asian J. 4, 1524–1526, 2009

    • Y. Nishioka, T. Yamaguchi, M. Kawano, M. Fujita Asymmetric [2+2] olefin cross photoaddition in a self-assembled host with remote chiral auxiliaries
      J. Am. Chem. Soc. 130, 8160–8161, 2008

    • T. Yamaguchi and M. Fujita
      Highly selective photo-mediated 1,4-radical addition to o-quinones controlled by a self-assembled cage
      Angew. Chem. Int. Ed. 47, 2067–2069, 2008

    • Y. Nishioka, T. Yamaguchi, M. Yoshizawa, M. Fujita
      Unusual [2+4] and [2+2] cycloadditions of arenes in the confined cavity of self-assembled cages
      J. Am. Chem. Soc. 129, 7000–7001, 2007

    • T. Yamaguchi, S. Tashiro, M. Tominaga, M. Kawano, T. Ozeki, M. Fujita
      Self-assembly and host-guest chemistry of a 3.5-nm coordination nanotube
      Chem. Asian J. 2, 468–476, 2007

    • T. Yamaguchi, S. Tashiro, M. Tominaga, M. Kawano, T. Ozeki, M. Fujita
      A 3.5-nm coordination nanotube
      J. Am. Chem. Soc. 126, 10818–10819, 2004