Structural and Functional analysis of RND type transporter

2009 Fiscal Year Final Research Report

• Project/Area Number: 19207009
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Tokyo Institute of Technology (2008-2009); Osaka University (2007)
• Principal Investigator: MURAKAMI Satoshi Tokyo Institute of Technology, 大学院・生命理工学研究科, 教授 (30300966)
• Project Period (FY): 2007 – 2009
• Keywords: 多剤排出トランスポーター / 結晶化 / X線結晶構造解析 / 多剤耐性 / 膜輸送

Research Abstract

Structure of AcrB was improved beyond 2.5Å resolution.
Along the substrate translocation pathway of AcrB, an important region where determine the substrate specificity was found.
Drug transport across the membrane was observed for Gram-positive RND transporter.

Research Products

• [Journal Article] Enhancement of femtosecond laser-induced nucleation of protein in a gel solution(043702) (2010)
  • Author(s): Ryota Murai, Hiroshi Y. Yoshikawa, Yoshinori Takahashi, Mihoko Maruyama, Shigeru Sugiyama, Gen Sazaki, Hiroaki Adachi, Kazufumi Takano, Hiroyoshi Matsumura, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori.
  • Journal Title: Appl. Phys. Lett. 96 Pages: 1-3
  • Peer Reviewed
• [Journal Article] Femtosecond laser processing of protein crystals grown in agarose gel (2009)
  • Author(s): Hitoshi Hasenaka, Shigeru Sugiyama, Mika Hirose, Noriko Shimizu, Tomoya Kitatani, Yoshinori Takahashi, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori, Hiroyoshi Matsumura.
  • Journal Title: J. Cryst. Growth 312 Pages: 73-78
  • Peer Reviewed
• [Journal Article] A Manipulating Tool for Protein Microcrystals in Solution Using Adhesive Materials(118001) (2009)
  • Author(s): Tomoya Kitatani, Hiroaki Adachi, Shigeru Sugiyama, Hiroyoshi Matsumura, Ryota Murai, Yoshinori Takahashi, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori, Kazufumi Takano.
  • Journal Title: Jpn. J. Appl. Phys. 48 Pages: 1-2
  • Peer Reviewed
• [Journal Article] Promotion of Crystal Nucleation of Protein by Semi-Solid Agarose Gel(125501) (2009)
  • Author(s): Kana Tanabe, Mika Hirose, Ryota Murai, Shigeru Sugiyama, Noriko Shimizu, Mihoko Maruyama, Yoshinori Takahashi, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Yusuke Mori, Eiichi Mizohata, Tsuyoshi Inoue, Hiroyoshi Matsumura.
  • Journal Title: Appl. Phys. Express 2 Pages: 1-3
  • Peer Reviewed
• [Journal Article] Growth of Large Protein Crystals by Top-Seeded Solution Growth Together with the Floating and Solution-Stirring Technique (2009)
  • Author(s): Noriko Shimizu, Shigeru Sugiyama, Mihoko Maruyama, Hiroshi Y. Yoshikawa, Yoshinori Takahashi, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Tsuyoshi Inoue Hiroyoshi Matsumura, Yusuke Mori.
  • Journal Title: Cryst. Growth Des. 9 Pages: 5227-5232
  • Peer Reviewed
• [Journal Article] Femtosecond Laser Processing of Agarose Gel Surrounding Protein Crystals for Development of an Automated Crystal Capturing System(105502) (2009)
  • Author(s): Shigeru Sugiyama, Hitoshi Hasenaka, Mika Hirose, Noriko Shimizu, Tomoya Kitatani, Yoshinori Takahashi, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori, Hiroyoshi Matsumura.
  • Journal Title: Jpn. J. Appl. Phys. 48 Pages: 1-5
  • Peer Reviewed
• [Journal Article] 多剤耐性 (2009)
  • Author(s): 村上聡
  • Journal Title: Multi-drug resistance Medical Science Digest 35 Pages: 346-347
  • Peer Reviewed
• [Journal Article] Protein Crystallization in Agarose Gel 4 with High Strength: Developing an Automated System for Protein Crystallographic Processes(075502) (2009)
  • Author(s): Shigeru Sugiyama, Kana Tanabe, Mika Hirose, Tomoya Kitatani, Hitoshi Hasenaka, Yoshinori Takahashi, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Yusuke Mori, Tsuyoshi Inoue, Hiroyoshi Matsumura.
  • Journal Title: Jpn. J. Appl. Phys. 48 Pages: 1-5
  • Peer Reviewed
• [Journal Article] Dynamic nature of disulfide bond formation catalysts revealed by crystal structures of DsbB (2009)
  • Author(s): Keiji Inaba, Satoshi Murakami, Atsushi Nakagawa, Hiroka Iida, Mai Kinjo, Koreaki Ito, Mamoru Suzuki.
  • Journal Title: EMBO J. 28 Pages: 779-791
  • Peer Reviewed
• [Journal Article] Femtosecond laser-induced nucleation of protein in agarose gel (2009)
  • Author(s): Hiroshi Y. Yoshikawa, Ryota Murai, Shigeru Sugiyama, Gen Sazaki, Tomoya Kitatani, Yoshinori Takahashi, Hiroaki Adachi, Hiroyoshi Matsumura, Satoshi Murakami, Tsuyoshi Inoue, Kazufumi Takano, Yusuke Mori.
  • Journal Title: J. Cryst. Growth 311 Pages: 956-959
  • Peer Reviewed
• [Journal Article] Evaluation and Improvement of a Technique to Manipulate Protein Crystals in Solution (2008)
  • Author(s): Tomoya Kitatani, Hiroaki Adachi, Shigeru Sugiyama, Hiroyoshi Matsumura, Ryota Murai, Yoshinori Takahashi, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori, Kazufumi Takano.
  • Journal Title: Jpn. J. Appl. Phys. 47 Pages: 8995-8997
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray crystallographic analysis of Ca2+-free primary Ca2+-sensor of Na+/Ca2+ exchanger (2008)
  • Author(s): Masashi Mima, Chika Kawai, Kumsun Paku, Koji Tomoo, Toshimasa Ishida, Shigeru Sugiyama, Hiroshi Matsumura, Tomoya Kitatani, Hiroshi Y. Yoshikawa, Syou Maki, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori, Satomi Kita, TakahMasashi Mima
  • Journal Title: Acta Crystallogr F64 Pages: 1125-1127
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary neutron diffraction studies of HIV-1 protease cocrystallized with inhibitor KNI-272 (2008)
  • Author(s): Hiroshi Matsumura, Motoyasu Adachi, Shigeru Sugiyama, Shino Okada, Megumi Yamakami, Taro Tamada, Koushi Hidaka, Yoshio Hayashi, Tooru Kimura, Yoshiaki Kiso, Tomoya Kitatani, Syou. Maki, Hiroshi Y. Yoshikawa, Hiroaki Adachi, Kazufumi Takano, Satoshi MurakaHiroshi Matsumura, Motoyasu Adachi, Shigeru Su
  • Journal Title: Acta Crystallogr. F64 Pages: 1003-1006
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment (2008)
  • Author(s): Shigeru Sugiyama, Yusuke Nomura, Taiichi Sakamoto, Tomoya Kitatani, Asako Kobayashi, Shin Miyakawa, Yoshinori Takahashi, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori, Yoshikazu Nakamura, Hiroyoshi Matsumura.
  • Journal Title: Acta Crystallogr. F64 Pages: 942-944
  • Peer Reviewed
• [Journal Article] Functional role of transmembrane Helix 6 in drug binding and transport by the ABC transporter MsbA (2008)
  • Author(s): Barbara Woebking, Saroj Velamakanni, Luca Federici, Markus A. Seeger, Satoshi Murakami, Hendrik van Veen.
  • Journal Title: Biochemistry. 47 Pages: 10904-10914
  • Peer Reviewed
• [Journal Article] Multidrug efflux transporter, AcrB-the pumping mechanism (2008)
  • Author(s): Satoshi Murakami
  • Journal Title: Curr. Opin. Struct. Biol 18 Pages: 459-465
  • Peer Reviewed
• [Journal Article] Laser energy dependence on femtosecond laser-induced nucleation of protein (2008)
  • Author(s): Hiroshi Y. Yoshikawa, Ryota Murai, Syou Maki, Tomoya Kitatani, Shigeru Sugiyama, Gen Sazaki, Hiroaki Adachi, Tsuyoshi Inoue, Hiroyoshi Matsumura, Kazufumi Takano, Satoshi Murakami, Takatomo Sasaki, Yusuke Mori.
  • Journal Title: Appl. Phys. A 93 Pages: 911-915
  • Peer Reviewed
• [Journal Article] Effect of solution flow by rotary shaker on protein crystallization (2008)
  • Author(s): Ryota Murai, Hiroshi Y. Yoshikawa, Hisato Kawahara, Syou Maki, Shigeru Sugiyama, Tomoya Kitatani, Hiroaki Adachi, Kazufumi Takano, Hiroyoshi Matsumura, Satoshi Murakami, Tsuyoshi Inoue, Takatomo Sasaki, Yusuke Mori.
  • Journal Title: J. Cryst. Growth 310 Pages: 2168-2172
  • Peer Reviewed
• [Journal Article] Protein crystallization in a 100 nl solution with new stirring equipment (2008)
  • Author(s): Syou Maki, Ryota Murai, Hiroshi Y. Yoshikawa, Tomoya Kitatani, Shinya Nakata, Hisato Kawahara, Hitoshi Hasenaka, Asako Kobayashi, Shino Okada, Shigeru Sugiyama, Hiroaki Adachi, Hiroshi Matsumura, Kazufumi Takano, Satoshi Murakami, Tsuyoshi Inoue, TakatomoSyou Maki, Ryota Mura
  • Journal Title: J. Synchrotron Rad. 15 Pages: 269-272
  • Peer Reviewed
• [Journal Article] New Technique of Manipulating a Protein Crystal Using Adhesive Material (2008)
  • Author(s): Tomoya Kitatani, Shigeru Sugiyama, Hiroyoshi Matsumura, Hiroaki Adachi, Hiroshi Y. Yoshikawa, Syou Maki, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori, Kazufumi Takano.
  • Journal Title: Appl. Phys. Express 1 Pages: 1-3
  • Peer Reviewed
• [Journal Article] ultidrug recognition and pumping by bacterial multidrug transporter ~ A structural view (2008)
  • Author(s): Satoshi Murakami
  • Journal Title: Protein Science 17 Pages: 1 68
  • Peer Reviewed
• [Journal Article] 多剤耐性の仕組み (2008)
  • Author(s): 村上聡
  • Journal Title: 日本臨床 66 Pages: 193-203
• [Journal Article] Crystal structures of a bacterial multidrug transporter reveal a functionally rotating mechanism. (2007)
  • Author(s): Satoshi Murakami, Akihito Yamaguchi
  • Journal Title: FEBS Journa 274Sup.1 Pages: 119
  • Peer Reviewed
• [Journal Article] 多剤排出トランスポーターの構造と機能結晶構造から明らかになった機能的回転メカニズム (2007)
  • Author(s): 村上聡
  • Journal Title: 蛋白質核酸酵素 52 Pages: 406-414
  • Peer Reviewed
• [Presentation] 細菌の薬剤耐性化機構の結晶学的解析Mechanism of bacterial multi-drug resistance based on the crystal structure of efflux transporter (2010)
  • Author(s): 村上聡
  • Organizer: 第83回日本細菌学会総会
  • Place of Presentation: 横浜
  • Year and Date: 20100327-20100329
• [Presentation] RNDtransporter, AcrB-Thepumping mechanism (2010)
  • Author(s): Satoshi Murakami
  • Organizer: 3rd FEBS Special Meeting『ATP-Binding Cassette Protein:From Multidrug Resistance to Genetic Diseases』
  • Place of Presentation: オーストリア
  • Year and Date: 20100227-20100305
• [Presentation] Structure and Function of Multi-drug Transporter AcrB (2010)
  • Author(s): Satoshi Murakami
  • Organizer: 4th INTERNATIONAL SYMPOSIUM ON RECENT TRENDS IN MACROMOLECULAR STRUCTURE AND FUNCTION
  • Place of Presentation: インド
  • Year and Date: 20100121-20100123
• [Presentation] Structure and Function of the Drug EffluxTransporter (2009)
  • Author(s): Satoshi Murakami
  • Organizer: 第一回台湾膜タンパク質・生物膜結晶構造生物学シンポジウム
  • Place of Presentation: 台湾
  • Year and Date: 20091209-20091210
• [Presentation] Multidrug Efflux Transporter-The Pumping Mechanism (2009)
  • Author(s): Satoshi Murakami
  • Organizer: 1st International Multidisciplinary Workshop『Membrane Biology Frontiers-Dynamics, Energy, Structure and Technology-』
  • Place of Presentation: ギリシャ
  • Year and Date: 20090528-20090602
• [Presentation] Transport by AcrB;a Structual approach (2009)
  • Author(s): Satoshi Murakami
  • Organizer: Gordon Reseach Conferences
  • Place of Presentation: アメリカ
  • Year and Date: 20090322-20090327
• [Presentation] 多剤排出輸送体の結晶構造に基づく多基質認識と輸送メカニズム (2009)
  • Author(s): 村上聡
  • Organizer: 第82回日本薬理学会年会
  • Place of Presentation: 横浜
  • Year and Date: 20090316-20090318
• [Presentation] 大腸菌多剤排出トランスポーターによる薬剤認識および排出機構 (2008)
  • Author(s): 村上聡
  • Organizer: 日本生物物理学会第46回年会
  • Place of Presentation: 福岡
  • Year and Date: 20081203-20081205
• [Presentation] Bacterial multi drug efflux transporter AcrB, -The pumping mechanism (2008)
  • Author(s): Satoshi Murakami
  • Organizer: XXI Congress of the International Union of Crystallography
  • Place of Presentation: 大阪
  • Year and Date: 20080823-20080831
• [Presentation] Multidrug Recognition and Pumping by Bacterial Multidrug Transporter-A structual View (2008)
  • Author(s): Satoshi Murakami
  • Organizer: 22nd Annual Symposium of The Protein Society
  • Place of Presentation: アメリカ
  • Year and Date: 20080719-20080723
• [Presentation] 大腸菌多剤排出トランスポーターによる薬剤認識および排出機構 (2008)
  • Author(s): 村上聡
  • Organizer: 第8回日本蛋白質科学会年会
  • Place of Presentation: 東京
  • Year and Date: 20080610-20080612
• [Presentation] 多剤排出トランスポーターによる多基質認識とその排出メカニズム (2008)
  • Author(s): 村上聡
  • Organizer: 第7回微生物研究会微生物研究会
  • Place of Presentation: 横浜
  • Year and Date: 2008-06-14
• [Presentation] 膜輸送体作動メカニズムの結晶学的解明 (2007)
  • Author(s): 村上聡、中島良介、松本崇、近藤洋平1、津田岳夫1、小川治夫1、豊島近1
  • Organizer: 第11回Spring8シンポジウム
  • Place of Presentation: 兵庫
  • Year and Date: 20071029-20071030
• [Presentation] Structure and mechanism of bacterial multi-drug efflux transporter (2007)
  • Author(s): Satoshi Murakami
  • Organizer: 24th European Crystallographic Meeting
  • Place of Presentation: モロッコ
  • Year and Date: 20070822-20070827
• [Presentation] Session1 Multi-Protein complex, Structural studies of multi-drug efflux transporter (2007)
  • Author(s): Satoshi Murakami
  • Organizer: 9th International Conference on Biology and Synchrotron Radiation
  • Place of Presentation: イングランド
  • Year and Date: 20070813-20070817
• [Presentation] Crystal structures of a bacterial multidrug transporter reveal a functionally rotating mechanism (2007)
  • Author(s): Satoshi Murakami
  • Organizer: 32nd FEBS Congress, Molecular Machines
  • Place of Presentation: オーストリア
  • Year and Date: 20070707-20070712
• [Presentation] 膜タンパク質を含むターゲット蛋白質の精製 (2007)
  • Author(s): 村上聡
  • Organizer: 千里ライフサイエンス技術講習会第47回「蛋白質X線構造解析技術～発現からデータ処理まで～」
  • Place of Presentation: 大阪
  • Year and Date: 2007-10-23
• [Presentation] Structure and mechanism of AcrAB bacterial multi-drug efflux pump (2007)
  • Author(s): Satoshi Murakami
  • Organizer: AstraZeneca Membran Protein Day(Seminar)
  • Place of Presentation: イングランド
  • Year and Date: 2007-08-20
• [Book] やさしい原理から入るタンパク質科学実験:Iタンパク質をつくる-抽出・精製と合成 (2008)
  • Author(s): 村上聡
  • Total Pages: 208,107-133
  • Publisher: 化学同人
• [Book] シリーズ生物薬科学実験講座 (2008)
  • Author(s): 村上聡
  • Total Pages: 250,89-107
  • Publisher: 廣川書店
• [Book] 生化学vol. 79 (2007)
  • Author(s): 村上聡
  • Total Pages: 542-549
  • Publisher: 日本生化学会
• [Patent(Industrial Property Rights)] 結晶製造方法、凍結結晶製造方法、結晶構造解析方法、結晶化スクリーニング方法、結晶化スクリーニング装置 (2008)
  • Inventor(s): 杉山成、安達宏昭、松村浩由、高野和文、村上聡、井上豪、森勇介
  • Industrial Property Rights Holder: 株式会社創晶(506243161)
  • Industrial Property Number: 特許権特願2008-008561
  • Filing Date: 2008-01-17
• [Patent(Industrial Property Rights)] 粘着式ピンセット、粘着式ピンセット用部材、粒子の保持方法、粒子の解析方法および分析装置 (2007)
  • Inventor(s): 安達宏昭、松村浩由、高野和文、村上聡、井上豪、森勇介、柴田和博、上野元信、山本浩司
  • Industrial Property Rights Holder: 有限会社シバタシステムサービス
  • Industrial Property Number: 特許権特願2007-296354
  • Filing Date: 2007-11-15
• [Patent(Industrial Property Rights)] 有機高分子結晶製造装置
  • Inventor(s): 杉山成、安達宏昭、松村浩由、高野和文、村上聡、井上豪、森勇介、国宗範彰
  • Industrial Property Rights Holder: 株式会社クニムネ
  • Industrial Property Number: 特許権特願2009-275465