NMR detection of conformational fluctuations of proteins and glycoconjugates for exploration of their correlations with biological functions

2012 Fiscal Year Final Research Report

• Project Area: Molecular Science of Fluctuations toward Biological Functions
• Project/Area Number: 20107004
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: National Institutes of Natural Sciences Okazaki Research Facilities
• Principal Investigator: KATO Koichi 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 岡崎統合バイオサイエンスセンター, 教授 (20211849)
• Project Period (FY): 2008 – 2012
• Keywords: NMR / 揺らぎ / 糖鎖 / タンパク質 / 複合糖質

Research Abstract

Using ultra-high field NMR spectroscopy in conjunction with other biophysical methods, we characterized conformational fluctuations of proteins and glycoconjugates as well as their complexes. In particular, we successfully developed novel methods for detailed analyses of dynamic interactions between glycolipid clusters and proteins associated with neurodegenerative disorders and dynamics of tertiary and quaternary structures of protein complexes involved in protein?fate determinations in cells. By applying the methods developed, we elucidated relationships between conformational fluctuations and functions of biomolecules.

Research Products

• [Journal Article] NMR characterization of interaction of GroEL with amyloid β as a model ligand. (2013)
  • Author(s): M.Yagi-Utsumi, T.Kunihara, T.Nakamura, Y.Uekusa, K.Makabe, K.Kuwajima, and K.Kato
  • Journal Title: FEBS Lett. Volume: 587 Pages: 605-609
  • DOI: DOI: 10.1016/j.febslet.2013.04.007
  • Peer Reviewed
• [Journal Article] Structural and functional mosaic nature of MHC class I molecules in their peptide-free form. (2013)
  • Author(s): E.Kurimoto, K.Kuroki, Y.Yamaguchi, M.Yagi-Utsumi, T.Igaki, T.Iguchi, K.Maenaka, and K.Kato
  • Journal Title: Mol. Immunol. Volume: 55 Pages: 393-399
  • DOI: DOI: 10.1016/j.molimm.2013.03.014
  • Peer Reviewed
• [Journal Article] Application of metabolic ^<13>C labeling in conjunction with high-field nuclear magnetic resonance spectroscopy for comparative conformational analysis of high mannose-type oligosaccharides. (2013)
  • Author(s): Y.Kamiya, K.Yanagi, T.Kitajima, T.Yamaguchi, Y.Chiba, and K.Kato
  • Journal Title: Biomolecules Volume: 3 Pages: 108-123
  • DOI: DOI:10.3390/biom3010108
  • Peer Reviewed
• [Journal Article] Ganglioside-embedding small bicelles for probing membrane-landing processes of intrinsically disordered proteins. (2013)
  • Author(s): T.Yamaguchi, T.Uno, Y.Uekusa, M.Yagi-Utsumi, and K.Kato
  • Journal Title: Chem. Commun. Volume: 49 Pages: 1235-1237
  • DOI: DOI: 10.1039/c2cc38016a
  • Peer Reviewed
• [Journal Article] Protein encapsulation within synthetic molecular hosts. (2012)
  • Author(s): D.Fujita, K.Suzuki, S.Sato, M.Yagi-Utsumi, Y.Yamaguchi, N.Mizuno, T.Kumasaka, M.Takata, M.Noda, S.Uchiyama, K.Kato, and M.Fujita
  • Journal Title: Nature Commun. Volume: 3 Pages: 1093
  • DOI: DOI: 10.1038/ncomms2093
  • Peer Reviewed
• [Journal Article] NMR characterization of the interaction between the PUB domain of peptide: N-glycanase and ubiquitin-like domain of HR23. (2012)
  • Author(s): Y.Kamiya, Y.Uekusa, A.Sumiyoshi, H.Sasakawa, T.Hirao, T.Suzuki, and K.Kato
  • Journal Title: FEBS Lett. Volume: 586 Pages: 1141-1146
  • DOI: DOI: 10.1016/j.febslet.2012.03.027
  • Peer Reviewed
• [Journal Article] Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations. (2012)
  • Author(s): S.Yamamoto, Y.Zhang, T.Yamaguchi, T.Kameda, and K.Kato
  • Journal Title: Chem. Commun. Volume: 48 Pages: 4752-4754
  • DOI: DOI: 10.1039/C2CC30353A
  • Peer Reviewed
• [Journal Article] A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex. (2012)
  • Author(s): H.Yagi, K.Ishimoto, T.Hiromoto, H.Fujita, T.Mizushima, Y.Uekusa, M.Yagi-Utsumi, E.Kurimoto, M.Noda, S.Uchiyama, F.Tokunaga, K. Iwai, and K.Kato
  • Journal Title: EMBO Rep. Volume: 13 Pages: 462-468
  • DOI: DOI: 10.1038/embor.2012.24
  • Peer Reviewed
• [Journal Article] Structural and molecular basis of carbohydrate?protein interaction systems as potential therapeutic targets. (2011)
  • Author(s): Y.Kamiya, M.Yagi-Utsumi, H.Yagi, and K.Kato
  • Journal Title: Curr. Pharm. Des. Volume: 17 Pages: 1672-1684
  • DOI: DOI: 10.2174/138161211796355074
  • Peer Reviewed
• [Journal Article] Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution. (2011)
  • Author(s): T.Hirano, O.Serve, M.Yagi-Utsumi, E.Takemoto, T.Hiromoto, T.Satoh, T.Mizushima, and K.Kato
  • Journal Title: J. Biol. Chem. Volume: 286 Pages: 37496-37502
  • DOI: DOI: 10.1074/jbc.M111.256354
  • Peer Reviewed
• [Journal Article] Kinetic asymmetry of subunit exchange of homooligomeric protein as revealed by deuteration-assisted small-angle neutron scattering. (2011)
  • Author(s): M.Sugiyama, E.Kurimoto, H.Yagi, K.Mori, T.Fukunaga, M.Hirai, G.Zaccai, and K.Kato
  • Journal Title: Biophys. J. Volume: 101 Pages: 2037-2042
  • DOI: DOI: 10.1016/j.bpj.2011.09.004
  • Peer Reviewed
• [Journal Article] Paramagnetic lanthanide tagging for NMR conformational analyses of N-linked oligosaccharides. (2011)
  • Author(s): S.Yamamoto, T.Yamaguchi, M.Erdelyi, C.Griesinger, and K.Kato
  • Journal Title: Chem. Euro. J. Volume: 17 Pages: 9280-9282
  • DOI: DOI: 10.1002/chem.201100856
  • Peer Reviewed
• [Journal Article] Overexpression of a homogeneous oligosaccharide with ^<13>C labeling by genetically engineered yeast strain. (2011)
  • Author(s): Y.Kamiya, S.Yamamoto, Y.Chiba, Y.Jigami, and K.Kato
  • Journal Title: J. Biomol. NMR Volume: 50 Pages: 397-401
  • DOI: DOI: 10.1007/s10858-011-9525-1
  • Peer Reviewed
• [Journal Article] Redox-dependent domain rearrangement of protein disulfide isomerase from a thermophilic fungus. (2010)
  • Author(s): M.Nakasako, A.Maeno, E.Kurimoto, T.Harada, Y.Yamaguchi, T.Oka, Y.Takayama, A.Iwata, and K.Kato
  • Journal Title: Biochemistry Volume: 49 Pages: 6953-6962
  • DOI: DOI: 10.1021/bi1006089
  • Peer Reviewed
• [Journal Article] Stable-isotope-assisted NMR approaches to glycoproteins using immunoglobulin G as a model system. (2010)
  • Author(s): K.Kato, Y.Yamaguchi, and Y.Arata
  • Journal Title: Progress in Nuclear Magnetic Resonance Spectroscopy Volume: 56 Pages: 346-359
  • DOI: DOI: 10.1016/j.pnmrs.2010.03.001
  • Peer Reviewed
• [Journal Article] NMR characterization of the interactions between lyso-GM1 aqueous micelles and amyloid β. (2010)
  • Author(s): M.Yagi-Utsumi, T.Kameda, Y.Yamaguchi, and K.Kato
  • Journal Title: FEBS Lett. Volume: 584 Pages: 831-836
  • DOI: DOI: 10.1016/j.febslet.2010.01.005
  • Peer Reviewed
• [Journal Article] Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency. (2010)
  • Author(s): M.Nishio, Y.Kamiya, T.Mizushima, S.Wakatsuki, H.Sasakawa, K.Yamamoto, S.Uchiyama, M.Noda, A.R.McKay, K.Fukui, H.-P.Hauri, and K.Kato
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 107 Pages: 4034-4039
  • DOI: DOI: 10.1073/pnas.0908526107
  • Peer Reviewed
• [Journal Article] Redox-dependent domain rearrangement of protein disulfide isomerase coupled with exposure of its substrate-binding hydrophobic surface. (2010)
  • Author(s): O.Serve, Y.Kamiya, A.Maeno, M.Nakano, C.Murakami, H.Sasakawa, Y.Yamaguchi, T.Harada, E.Kurimoto, M.Yagi-Utsumi, T.Iguchi, K.Inaba, J.Kikuchi, O.Asami, T.Kajino, T.Oka, M.Nakasako, and K.Kato
  • Journal Title: J. Mol. Biol. Volume: 396 Pages: 361-374
  • DOI: DOI:10.1016/j.jmb.2009.11.049
  • Peer Reviewed
• [Journal Article] Crystal structure of UbcH5b-ubiquitin intermediate: Insight into the formation of the self-assembled E2-Ub conjugates. (2010)
  • Author(s): E.Sakata, T.Satoh, S.Yamamoto, Y.Yamaguchi, M.Yagi-Utsumi, E.Kurimoto, K.Tanaka, S.Wakatsuki, and K.Kato
  • Journal Title: Structure Volume: 18 Pages: 138-147
  • DOI: DOI:10.1016/j.str.2009.11.007
  • Peer Reviewed
• [Journal Article] Human OS-9, a lectin required for glycoprotein endoplasmic reticulum-associated degradation, recognizes mannose-trimmed N-glycans. (2009)
  • Author(s): N.Hosokawa, Y.Kamiya, D.Kamiya, K.Kato, and K.Nagata
  • Journal Title: J. Biol. Chem. Volume: 284 Pages: 17061-17068
  • DOI: DOI:10.1074/jbc.M809725200
  • Peer Reviewed
• [Journal Article] Up-and-down topological mode of amyloid β-peptide lying on hydrophilic/hydrophobic interface of ganglioside clusters. (2009)
  • Author(s): M.Utsumi, Y.Yamaguchi, H.Sasakawa, N.Yamamoto, K.Yanagisawa, and K.Kato
  • Journal Title: Glycoconjugate J. Volume: 26 Pages: 999-1006
  • DOI: DOI:10.1007/s10719-008-9216-7
  • Peer Reviewed
• [Presentation] Molecular and structural basis for N-glycan-depepndent determination of glycoprotein fates in cells. (2013)
  • Author(s): K.Kato
  • Organizer: Glycobiology, Gordon Research Conference
  • Place of Presentation: Ventura (USA)
  • Year and Date: 2013-03-04
• [Presentation] Structural Views of Carbohydrate-Protein Interaction Systems as Potential Therapeutic Targets. (2013)
  • Author(s): K.Kato
  • Organizer: Pure and Applied Chemistry International Conference 2013 (PACCON 2013)
  • Place of Presentation: Chon Buri (Thailand)
  • Year and Date: 2013-01-24
• [Presentation] Structural views of carbohydrate-protein interaction systems as potential therapeutic targets. (2012)
  • Author(s): K.Kato
  • Organizer: 26 International Carbohydrate Symposium
  • Place of Presentation: Madrid (Spain)
  • Year and Date: 2012-07-26
• [Presentation] A systematic approach for structural glycoproteomics. (2011)
  • Author(s): K.Kato
  • Organizer: The 23rd Annual Meeting of the Korean Society for Molecular and Cellular Biology
  • Place of Presentation: Seoul (Korea)
  • Year and Date: 2011-10-07
• [Presentation] Structural and dynamics views of the ubiquitin-proteasome system. (2011)
  • Author(s): K.Kato
  • Organizer: The 11^<th> KIAS Conference on Protein Structure and Function
  • Place of Presentation: Seoul (Korea)
  • Year and Date: 2011-10-06
• [Presentation] Structural and molecular basis of carbohydrate-protein interaction systems as potential therapeutic targets. (2011)
  • Author(s): K.Kato
  • Organizer: 第31回内藤コンファレンス
  • Place of Presentation: シャトレーゼガトーキングダムサッポロ(北海道)
  • Year and Date: 2011-09-15
• [Presentation] Sugar-protein interaction systems as potential therapeutic targets. (2011)
  • Author(s): K.Kato
  • Organizer: 98^<th> Indian Science Congress
  • Place of Presentation: Chennai (India)
  • Year and Date: 2011-01-05
• [Presentation] NMR characterization of conformations, dynamics, and interactions of glycoconjugates. (2010)
  • Author(s): K.Kato
  • Organizer: The 25th International Carbohydrate Symposium
  • Place of Presentation: 幕張メッセ(千葉)
  • Year and Date: 2010-08-03
• [Presentation] Stable-isotope-assisted NMR approaches to structural glycomics. (2009)
  • Author(s): K.Kato
  • Organizer: 20^<th> International Symposium on Glycoconjugates
  • Place of Presentation: San Juan (Puerto Rico)
  • Year and Date: 2009-11-30
• [Presentation] Structural Glycobiology by NMR and Sugar Library Approaches. (2009)
  • Author(s): K.Kato
  • Organizer: 3rd Asia-Pacific NMR symposium
  • Place of Presentation: Jeju (Korea)
  • Year and Date: 2009-10-27
• [Book] Glycoproteins and antibodies: Solution NMR studies. Encyclopedia of Magnetic Resonance (R.K.Harris and R.E.Wasylishen ed.) vol.3 (2012)
  • Author(s): K.Kato and Y.Yamaguchi
  • Total Pages: 1779-1790
  • Publisher: John Wiley (Chichester)
• [Book] Redox-dependent chaperoning, following PDI footsteps. Protein Folding (E.C.Walters ed.) (2011)
  • Author(s): O.Serve, Y.Kamiya, and K.Kato
  • Total Pages: 489-500
  • Publisher: NOVA Science Publishers (New York)
• [Book] 神経変性疾患にかかわる天然変性タンパク質の分子構造ダイナミクス.MedicalBio別冊揺らぎと生体機能(寺嶋正秀編) (2010)
  • Author(s): 加藤晃一, 矢木真穂
  • Total Pages: 32-37
  • Publisher: オーム社
• [Book] NOVA Science Publishers (New York) (2009)
  • Author(s): Y.Kamiya, D.Kamiya, R.Urade, T.Suzuki, and K.Kato
  • Total Pages: 27-40
  • Publisher: Sophisticated modes of sugar recognition by intracellular lectins involved in quality control of glycoproteins. Glycobiology Research Trends (G.Powell and O.McCabe ed.),
• [Book] 細胞内レクチンによる糖蛋白質の輸送と品質管理の構造基盤.糖鎖情報の独自性と普遍性(古川鋼一,遠藤玉夫,岡昌吾,本家孝一,加藤晃一編集) (2009)
  • Author(s): 神谷由紀子, 加藤晃一
  • Total Pages: 1662-1669
  • Publisher: 共立出版
• [Remarks] 研究成果に関するweb ページ
  • URL: http://www.ims.ac.jp/topics/2012/121001.html
• [Remarks]
  • URL: http://www.ims.ac.jp/topics/2010/110217.html
• [Remarks]
  • URL: http://www.ims.ac.jp/topics/2009/100215.html
• [Remarks]
  • URL: http://www.ims.ac.jp/topics/2009/100118.html
• [Remarks] 新聞報道日経産業新聞 2012年10月3日
• [Remarks] 日刊工業新聞 2012年10月3日
• [Remarks] 化学工業日報 2012年10月3日
• [Remarks] 薬事日報 2012年5月25日
• [Remarks] 中日新聞 2011年11月30日
• [Remarks] 科学新聞 2010年3月5日
• [Remarks] 日経産業新聞 2010年2月16日
• [Remarks] 科学新聞 2010年1月29日
• [Remarks] 日経産業新聞 2010年1月19日
• [Patent(Industrial Property Rights)] 残余双極子相互作用の解析方法及び残余双極子相互作用解析用試薬 (2009)
  • Inventor(s): 藤田誠, 佐藤宗太, 諸原理, 加藤晃一, 山口芳樹
  • Industrial Property Rights Holder: 国立大学法人東京大学, 大学共同利用機関法人自然科学研究機構, 独立行政法人理化学研究所
  • Industrial Property Number: 特願2009-057080
  • Filing Date: 2009-03-10