Structural analysis of cell adhesion molecules that determine cell coordinate in tissue

• Project/Area Number: 26440028
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Osaka University
• Principal Investigator: Suzuki Mamoru 大阪大学, たんぱく質研究所, 准教授 (40280507)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: ネクチン / 構造生物学 / 結晶構造解析 / 細胞接着分子 / Ｘ線結晶構造解析

Outline of Final Research Achievements

We established recombinant expression systems for extracellular domains of mouse Nectin-1 and mouse Nectin-3 in insect cell Sf-9. First we tried to purify Nectin-1 / Nectin-3 heterodimer fraction from the mixture of cultural supernatants. However, the result of surface plasmon resonance analysis indicated the fast dissociation rate constant of heterophilic interaction between Nectin-1 and Nectin-3, suggested difficulty of stable hetero-complex purification. Thus we next established individual purification systems for Nectin-1 and Nectin-3, respectively. The purified Nectins were mixed and used for crystallization experiments. As a result, structures of Nectin-1 homodimer and Nectin-3 homodimer were obtained from mixture of purified Nectin-1 and Nectin-3 in 2.24 A and 2.58 A resolutions, respectively (PDB ID: 5B21and 5B22). Additionally, chemical crosslink experiment using BS3 crosslinker revealed that the minimal unit of Nectin-1 / Nectin-3 heterophilic complex is heterodimer.

Research Products

• [Journal Article] Hydroxyethyl cellulose matrix applied to serial crystallography. (2017)
  • Author(s): Michihiro Sugahara, Takanori Nakane, Tetsuya Masuda, Mamoru Suzuki, Shigeyuki Inoue, Changyong Song, Rie Tanaka, Toru Nakatsu, Eiichi Mizohata, Fumiaki Yumoto, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, Keiji Numata, Eriko Nango, So Iwata
  • Journal Title: Scientific reports Volume: 7 Issue: 1 Pages: 703-703
  • DOI: 10.1038/s41598-017-00761-0
  • NAID: 120006223637
  • Peer Reviewed / Open Access
• [Journal Article] Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL. (2017)
  • Author(s): Suga, M.†, Akita, F.†, Sugahara, M.†, Kubo, M.†, Nakajima, Y.† et al. (†equal contribution)(38人中1番目)
  • Journal Title: Nature Volume: 543 Issue: 7643 Pages: 131-135
  • DOI: 10.1038/nature21400
  • NAID: 120006344935
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Atomic resolution structure of serine protease proteinase K at ambient temperature (2017)
  • Author(s): Tetsuya Masuda, Mamoru Suzuki, Shigeyuki Inoue, Changyong Song, Takanori Nakane, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Bunzo Mikami, Osamu Nureki, Keiji Numata, So Iwata, Michihiro Sugahara
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 45604-45604
  • DOI: 10.1038/srep45604
  • NAID: 120006027152
  • Peer Reviewed
• [Journal Article] Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent (2016)
  • Author(s): Takanori Nakane, Shinya Hanashima, Mamoru Suzuki, Haruka Saiki, Taichi Hayashi, Keisuke Kakinouchi, Shigeru Sugiyama, Satoshi Kawatake, Shigeru Matsuoka, Nobuaki Matsumori, et al
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 113 Issue: 46 Pages: 13039-13044
  • DOI: 10.1073/pnas.1602531113
  • Peer Reviewed / Open Access
• [Journal Article] Structural characterization of an aldo-keto reductase (AKR2E5) from the silkworm Bombyx mori (2016)
  • Author(s): Yamamoto K., Higashiura A., Suzuki M., Shiotsuki T., Sugahara R., Fujii T., Nakagawa A.
  • Journal Title: Biochemical and Biophysical Research Communications Volume: 474 Issue: 1 Pages: 104-110
  • DOI: 10.1016/j.bbrc.2016.04.079
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography. (2016)
  • Author(s): Fukuda Y, Tse KM, Nakane T, Nakatsu T, Suzuki M, Sugahara M, Inoue S, Masuda T, Yumoto F, Matsugaki N, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Murphy ME, Inoue T, Iwata S, Mizohata E.
  • Journal Title: PNAS Volume: 113 Issue: 11 Pages: 2828-2933
  • DOI: 10.1073/pnas.1517770113
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Oil-free hyaluronic acid matrix for serial femtosecond crystallography (2016)
  • Author(s): Michihiro Sugahara, Changyong Song, Mamoru Suzuki, Tetsuya Masuda, Shigeyuki Inoue, Takanori Nakane, Fumiaki Yumoto, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, Keiji Numata & So Iwata
  • Journal Title: Scientific Reports Volume: 6 Issue: 1 Pages: 24484-24484
  • DOI: 10.1038/srep24484
  • NAID: 120005749903
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography. (2016)
  • Author(s): Fukuda Y, Tse KM, Suzuki M, Diederichs K, Hirata K, Nakane T, Sugahara M, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Matsumura H, Inoue T, Iwata S, Mizohata E.
  • Journal Title: J. Biochem Volume: 未定 Issue: 5 Pages: 527-538
  • DOI: 10.1093/jb/mvv133
  • NAID: 40020833586
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Native sulfur/chlorine SAD phasing for serial femtosecond crystallography. (2015)
  • Author(s): Nakane T, Song C, Suzuki M, Nango E, Kobayashi J, Masuda T, Inoue S, Mizohata E, Nakatsu T, Tanaka T, Tanaka R, Shimamura T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Nureki O, Iwata S, Sugahara M.
  • Journal Title: Acta Crystallogr D Biol Crystallogr. Volume: 71 Issue: 12 Pages: 2519-25
  • DOI: 10.1107/s139900471501857x
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. (2015)
  • Author(s): Atsushi Kodan, Tomohiro Yamaguchi, Tomohiro Murai, Keiko Gomi, Naoki Kajiyama, Eiichi Mizohata, Mamoru Suzuki, Eriko Nango, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Jaehyun Park, Changyong Song, Takaki Hatsui, Makina Yabashi, So Iwata, Hiroaki Kato, Hideo Ago, Masaki Yamamoto & Toru Nakatsu
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 14017-14017
  • DOI: 10.1038/srep14017
  • NAID: 120005651939
  • Peer Reviewed / Open Access
• [Journal Article] Diverse application platform for hard X-ray diffraction in SACLA (DAPHNIS): application to serial protein crystallography using an X-ray free-electron laser. (2015)
  • Author(s): Tono K, Shimamura T, et al.
  • Journal Title: J. Synchrotron Rad. Volume: 22 Issue: 3 Pages: 532-537
  • DOI: 10.1107/s1600577515004464
  • Peer Reviewed
• [Journal Article] Crystal structure of afadin PDZ domain-nectin-3 complex shows the structural plasticity of the ligand-binding site. (2015)
  • Author(s): Fujiwara Y, Goda N, Tamashiro T, Narita H, Satomura K, Tenno T, Nakagawa A, Oda M, Suzuki M, Sakisaka T, Takai Y, Hiroaki H.
  • Journal Title: Protein Sci. Volume: 24 Issue: 3 Pages: 376-385
  • DOI: 10.1002/pro.2628
  • Peer Reviewed / Open Access
• [Journal Article] Effect of the replacement of aspartic acid/glutamic acid residues with asparagine/glutamine residues in RNase He1 from Hericium erinaceus on inhibition of human leukemia cell lineproliferation. (2015)
  • Author(s): Kobayashi H, Motoyoshi N, Itagaki T, Suzuki M, Inokuchi N.
  • Journal Title: Biosci.Biotechnol.Biochem. Volume: 79 Issue: 2 Pages: 211-217
  • DOI: 10.1080/09168451.2014.972327
  • Peer Reviewed
• [Journal Article] Grease matrix as a versatile carrier of proteins for serial crystallography. (2015)
  • Author(s): Sugahara M, Shimamura T, et al.
  • Journal Title: Nat Methods. Volume: 12 Issue: 1 Pages: 61-63
  • DOI: 10.1038/nmeth.3172
  • NAID: 120005682565
  • Peer Reviewed
• [Journal Article] Protein Structure Analyses Using X-ray Free-Electron Lasers. (2014)
  • Author(s): Mizohata E, Nango E, Sugahara M, Suzuki M, and Iwata S.
  • Journal Title: J Cryst Soc Jap. Volume: 56 Pages: 241-246
  • NAID: 130004688356
  • Peer Reviewed
• [Journal Article] In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology? (2014)
  • Author(s): Gallat Francois-Xavier, N. Matsugaki, P. Coussens Nathan, Yagi J. K., Boudes M., T. Higashi, Daisuke Tsuji, Tatano Yutaka, M. Suzuki, E. Mizohata, K. Tono, Y. Hatui, M. Yabashi, E. Nango, K.Itou, Coulibaly Fasseli, Tobe Stephen, Ramaswamy S., S. Iwata and Chavas M. L.
  • Journal Title: The Royal Society Volume: 369 Issue: 1647 Pages: 20130497-20130497
  • DOI: 10.1098/rstb.2013.0497
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] X-Ray Crystallographic Structure of RNase Po1 That Exhibits Antitumor Activity. (2014)
  • Author(s): Hiroko Kobayashi,Takuya Katsutani, Yumiko Hara, Naomi Motoyoshi, Tadashi Itagaki, Fusamichi Akita, Akifumi Higashiura, Yusuke Yamada, Norio Inokuchi and Mamoru Suzuki
  • Journal Title: Biol. Pharm. Bull. Volume: 37 Pages: 968-978
  • NAID: 130004147340
  • Peer Reviewed
• [Journal Article] Radically different thioredoxin domain arrangement of ERp46, an efficient disulfi de-bond introducer of the mammalian PDI family (2014)
  • Author(s): Kojima, R., Okumura, M., Masui. S., et al.
  • Journal Title: Structure Volume: 22 Issue: 3 Pages: 431-443
  • DOI: 10.1016/j.str.2013.12.013
  • Peer Reviewed / Open Access
• [Presentation] ヤマブシタケ由来RNaseHe1のZn複合体のX線構造解析 (2017)
  • Author(s): 小林弘子, 元吉尚美, 板垣正, 武部克希, 寒川剛, 鈴木守
  • Organizer: 日本薬学会第137年会
  • Place of Presentation: 宮城県仙台市仙台国際センター
  • Year and Date: 2017-03-24
• [Presentation] M3型化膿レンサ球菌が産生する線毛タンパク質 FctA3 の結晶構造解析 (2016)
  • Author(s): 川剛、武部克希、中田匡宣、川端重忠、鈴木守
  • Organizer: 日本結晶学会平成28年度年会
  • Place of Presentation: 茨城県水戸市茨城県民文化センター
  • Year and Date: 2016-11-17
• [Presentation] 高粘度結晶輸送媒体を利用したXFEL施設SACLAでの連続フェムト秒結晶構造解析 (2016)
  • Author(s): 菅原道泰，鈴木 守，桝田 哲哉，井上茂之，Changyong Song,中根崇智，溝端栄一,中津亨, 湯本史明, 南後恵理子, 登野健介, 沼田 圭司，岩田想
  • Organizer: 日本結晶学会平成28年度年会
  • Place of Presentation: 茨城県水戸市茨城県民文化センター
  • Year and Date: 2016-11-17
• [Presentation] 膜蛋白質のSFXによる迅速位相決定を志向したヨウ素含有界面活性剤の開発 (2016)
  • Author(s): 中根崇智、花島慎弥、鈴木守、斎木悠、林太一、垣之内啓介、杉山成、川竹悟史、松岡茂、松森信明、南後恵理子、小林淳、島村達郎、木村香菜子、森千寿、国島直樹、菅原道泰、高久陽子、井上茂之、桝田哲哉、保坂俊彰、 登野健介、城地保昌、亀島敬、初井宇記、矢橋牧名、井上豪、濡木理、岩田想、村田道雄、溝端栄一
  • Organizer: 日本結晶学会平成28年度年会
  • Place of Presentation: 茨城県水戸市茨城県民文化センター
  • Year and Date: 2016-11-17
• [Presentation] 細胞接着因子 Nectin-1/3 ヘテロ複合体の立体構造解析 (2016)
  • Author(s): 寒川剛、武部克希、勝谷拓也、鈴木守
  • Organizer: 第16回日本蛋白質科学会年会
  • Place of Presentation: 福岡県福岡市福岡国際会議場
  • Year and Date: 2016-06-07
• [Presentation] X線自由電子レーザーを用いた新規タンパク質の立体構造決定 (2016)
  • Author(s): 山下恵太郎, 潘 東青, 奥田智彦, 菅原道泰, 小段篤史, 山口知宏, 村井智洋, 溝端栄一, 鈴木 守, 南後恵理子, 登野健介, 城地保昌, 亀島 敬, 初井宇記, 矢橋牧名, 岩田 想, 加藤博章, 吾郷日出夫, 山本雅貴, 中津 亨
  • Organizer: 日本薬学会第136年会
  • Place of Presentation: パシフィコ横浜（神奈川県横浜市）
  • Year and Date: 2016-03-26
• [Presentation] ヤマブシタケ由来 RNase He1 の改変による至適 pHの変動について (2016)
  • Author(s): 小林弘子, 元吉尚美, 板垣 正, 鈴木 守, 井口法男
  • Organizer: 日本薬学会第136年会
  • Place of Presentation: パシフィコ横浜（神奈川県横浜市）
  • Year and Date: 2016-03-26
• [Presentation] fimA P. gingivalis Ⅱ型 TDC60株産生ジペプチダーゼの構造および呼吸器官への為害性 (2015)
  • Author(s): 菱沼光恵，田中陽子，矢口 学，桒原紀子，鈴木 守，野本たかと
  • Organizer: 日本障害者歯科学会
  • Place of Presentation: 名古屋国際会議場（愛知県名古屋市）
  • Year and Date: 2015-11-06
• [Presentation] 細胞接着因子ネクチンのヘテロ複合体の結晶構造解析 (2015)
  • Author(s): 寒川剛、武部克希、鈴木守
  • Organizer: 日本結晶学会平成27年度年会
  • Place of Presentation: 大阪府立大学 中百舌鳥キャンパス（大阪府堺市）
  • Year and Date: 2015-10-17
• [Presentation] シリアル結晶学における重原子誘導体を用いた位相決定 (2015)
  • Author(s): 山下恵太郎・潘東青・長谷川和也・菅原道泰・村井智洋・小段篤史・溝端栄一・鈴木 守・桝田哲哉・平田邦生・加藤博章・吾郷日出夫・熊坂 崇・山本雅貴・中津亨
  • Organizer: 日本結晶学会平成27年度年会
  • Place of Presentation: 大阪府立大学 中百舌鳥キャンパス（大阪府堺市）
  • Year and Date: 2015-10-17
• [Presentation] 甘味タンパク質ソーマチンの連続フェムト秒結晶構造解析 (2015)
  • Author(s): 桝田 哲哉、南後 恵理子、菅原 道泰、鈴木 守、登野 健介、城地 保昌、亀島 敬、Park Jaehyun、Song Changyong、初井 宇記、矢橋 牧名、大久保 喬平、三上 文三、北畠 直文、谷 史人、岩田 想
  • Organizer: 日本農芸化学会2015年度大会
  • Place of Presentation: 岡山
  • Year and Date: 2015-03-26 – 2015-03-29
• [Presentation] システイン残基改変体を用いたヤマブシタケ由来RNase He1の安定性の検討 (2015)
  • Author(s): 小林弘子、元吉尚美、板垣 正、鈴木 守、井口法男
  • Organizer: 日本薬学会第135年会
  • Place of Presentation: 神戸
  • Year and Date: 2015-03-25 – 2015-03-28
• [Presentation] 歯周病原因菌由来HBP35の構造と機能 (2015)
  • Author(s): 鈴木 守、柴田恭子、 安孫子宜光
  • Organizer: 物構研サイエンスフェスタ
  • Place of Presentation: つくば
  • Year and Date: 2015-03-17 – 2015-03-18
• [Presentation] 特異的細胞接着の構造生物学的理解を目指して (2014)
  • Author(s): 寒川剛・成田宏隆・勝谷拓也・中川敦史・鈴木守
  • Organizer: 日本結晶学会平成26年度年会
  • Place of Presentation: 東京
  • Year and Date: 2014-11-01 – 2014-11-03
• [Presentation] アドヘレンスジャンクションで働く接着因子の立体構造と機能 (2014)
  • Author(s): 鈴木 守
  • Organizer: 第56回歯科基礎医学会学術大会
  • Place of Presentation: 福岡
  • Year and Date: 2014-09-25 – 2014-09-27
• [Remarks] 鈴木守ユニット
  • URL: http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/index.html
• [Remarks] 大阪大学蛋白質研究所 鈴木守
  • URL: http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/