Studies on the correlation between the internal dynamics and hydration of proteins by X-ray crystallography for humidity-controlled protein crystals

• Project/Area Number: 19204042
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biophysics/Chemical physics
• Research Institution: Keio University
• Principal Investigator: NAKASAKO Masayoshi Keio University, 理工学部, 教授 (30227764)
• Project Period (FY): 2007 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥36,010,000 (Direct Cost: ¥27,700,000、Indirect Cost: ¥8,310,000); Fiscal Year 2008: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000); Fiscal Year 2007: ¥26,000,000 (Direct Cost: ¥20,000,000、Indirect Cost: ¥6,000,000)
• Keywords: 生物物理 / ナノマシン / 表面・界面物性 / 放射線・X線・粒子線 / 生体分子 / 蛋白質水和 / 蛋白質結晶学 / 湿度制御 / 光受容蛋白質 / 脱炭酸酵素 / 分子動力学計算 / 脱水素酵素 / 受容体蛋白質

Research Abstract

蛋白質結晶周辺の湿度を変化させ、結晶内のバルク水量を非破壊・可逆的に制御可能な装置の開発を進め、湿潤空気流量300~450ml/minで相対湿度20~96%rhの範囲で実験を行うことが可能な装置とその実験手順を確立し各種蛋白質結晶に適用した。サブゼロ温度領域で蛋白質のダイナミクスを探る実験、種々の蛋白質結晶についての構造解析、分子動力学計算を通じた蛋白質の運動と水和構造変化の相関解析も実施した。

Research Products

• [Journal Article] タンパク質内部運動に伴う水和構造変化を探る (2008)
  • Author(s): 中迫雅由
  • Journal Title: 日本結晶学会誌(解説,責任著者) 51 Pages: 37-39
  • NAID: 10024820285
  • Peer Reviewed
• [Journal Article] Structural basis of LOV1-dimerization of Arabidopsis phototropin 1 and 2 (2008)
  • Author(s): Masayoshi Nakasako, Kazunori Zikihara, Daisuke Matsuoka, Hitomi Katsura, Satoru Tokutomi
  • Journal Title: J. Mol. Biol.(Cover Illustration)(責任著者)(科学新聞他掲載) 381 Pages: 718-733
  • NAID: 130006993861
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus (2008)
  • Author(s): Masayoshi Nakasako, Michihiro Hirata, Nobutaka Shimizu, Syuntaro Hosokawa, DaisukeMatsuoka, Masaki Yamamoto and Satoru Tokutomi
  • Journal Title: Acta Crystallogra F(責任著者) 64 Pages: 610-613
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction experiments of LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana (2008)
  • Author(s): Masayoshi Nakasako, Rika Obata, Ryosuke Okubo, Shyuichi Nakayama, Kenji Miyamoto and Hiromichi Ohta
  • Journal Title: Acta Crystallogra F(責任著者) 64 Pages: 617-621
  • Peer Reviewed
• [Journal Article] タンパク質の水和構造を探る (2008)
  • Author(s): 中迫雅由
  • Journal Title: Molecular Science Journal(責任著者) 2, A0022 Pages: 7-7
  • NAID: 130002126190
  • Peer Reviewed
• [Journal Article] 非弾性散乱の生物への応用について (2008)
  • Author(s): 城地保昌、中迫雅由、難波啓一
  • Journal Title: 日本結晶学会誌(解説) 50 Pages: 78-82
  • NAID: 10021085479
  • Peer Reviewed
• [Journal Article] タンパク質内部運動に伴う水和構造変化を探る (2008)
  • Author(s): 中迫雅由
  • Journal Title: 日本結晶学会誌 51 Pages: 37-39
  • NAID: 10024820285
  • Peer Reviewed
• [Journal Article] Structural basis of LOV1-dimerization of Arabidopsis phototropin 1 and 2 (2008)
  • Author(s): M. Nakasako, et al.
  • Journal Title: Journal of Molecular Biology 381 Pages: 718-733
  • NAID: 130006993861
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction experiments of arylma lonate decarboxylase from Alcaligenes bronchisepticus (2008)
  • Author(s): M. Nakasako, et al.
  • Journal Title: Acta Crystallographica F64 Pages: 610-613
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction experiments of LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana (2008)
  • Author(s): M. Nakasako, et al.
  • Journal Title: Ada Crystallographica F64 Pages: 617-621
  • Peer Reviewed
• [Journal Article] タンパク質の水和構造を探る (2008)
  • Author(s): 中迫雅由
  • Journal Title: Molecular Science Journal 2
  • NAID: 130002126190
  • Peer Reviewed
• [Journal Article] 非弾性散乱の生物への応用について (2008)
  • Author(s): 城地保昌, 中迫雅由, 難波啓一
  • Journal Title: 日本結晶学会誌 50 Pages: 78-82
  • NAID: 10021085479
  • Peer Reviewed
• [Journal Article] タンパク質の水和構造を探る (2008)
  • Author(s): 中迫 雅由
  • Journal Title: Molecular Science Journal 2
  • NAID: 130002126190
  • Peer Reviewed
• [Journal Article] 非弾性散乱の生物への応用について (2008)
  • Author(s): 城地 保昌、中迫 雅由、難波 啓一
  • Journal Title: 日本結晶学会誌 50 Pages: 78-82
  • NAID: 10021085479
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus (2008)
  • Author(s): Masayoshi Nakasako, Rika Obata, Ryosuke Okubo, Shyuichi Nakayama, Kenji Miyamoto and Hiromichi Ohta
  • Journal Title: Acta Crystallographica Section F (掲載確定)
  • Peer Reviewed
• [Journal Article] Structural basis of LOV1-dimerization of phototropin 1 and 2 from Arabidopsis thaliana (2008)
  • Author(s): Masayoshi Nakasako, Kazunori Zikihara, Daisuke Matsuoka, Hitomi Katsura and Satoru Tokutomi
  • Journal Title: Journal of Molecular Biology (掲載確定)
  • Peer Reviewed
• [Journal Article] Crystal Structures of Blasticidin S Deaminase (BSD) : Implications for Dynamic Properties of Catalytic Zinc (2007)
  • Author(s): Takashi Kumasaka, Masaki Yamamoto,Makio Furuichi, Masayoshi Nakasako, Aik-Hong Teh, Makoto Kimura, Isamu Yamaguchi, Tatzuo Ueki
  • Journal Title: J. Biol. Chem. 228 Pages: 37103-37111
  • Peer Reviewed
• [Journal Article] Crystal Structures of Blasticidin S Deaminase(BSD):Implications for Dynamic Properties of Catalytic Zinc (2007)
  • Author(s): Takashi Kumasaka, Masaki Yamamoto, Makio Furuichi, Masayoshi Nakasako, Aik-Hong Teh, Makoto Kimura, Isamu Yamaguchi, Tatzuo Ueki
  • Journal Title: Journal of Biological Chemistry 228 Pages: 37103-37111
  • Peer Reviewed
• [Presentation] 蛋白質結晶湿度制御装置の開発 (2009)
  • Author(s): 高山裕貴,中迫雅由
  • Organizer: 第22 回日本放射光学会年会
  • Place of Presentation: 東京
  • Year and Date: 2009-01-12
• [Presentation] 蛋白質結晶湿度制御装置の開発 (2009)
  • Author(s): 高山裕貴, 中迫雅由
  • Organizer: 第22回日本放射光学会年会
  • Place of Presentation: 東京大学
  • Year and Date: 2009-01-12
• [Presentation] 細胞の空間階層X線イメージングの現在と未来への期待 (2008)
  • Author(s): 中迫雅由
  • Organizer: 自然科学研究機構H20 年度自然科学における階層と全体シンポジウム
  • Place of Presentation: 蒲郡
  • Year and Date: 2008-12-16
• [Presentation] 細胞の空間階層X線ィメージングの現在と未来への期待(招待講演) (2008)
  • Author(s): 中迫雅由
  • Organizer: 自然科学研究機構平成20年度"自然科学における階層と全体シンポジウム
  • Place of Presentation: 蒲郡、愛知
  • Year and Date: 2008-12-16
• [Presentation] 蛋白質の運動と連動する水和水のコヒーレントな集団運動の探索 (2008)
  • Author(s): 中迫雅由
  • Organizer: 特定領域「高次系分子科学」第2回公開シンポジウム
  • Place of Presentation: 大阪
  • Year and Date: 2008-11-11
• [Presentation] データベース解析に基づく蛋白質の水和構造予測 (2008)
  • Author(s): 松岳大輔、中迫雅由
  • Organizer: 特定領域「高次系分子科学」第2 回公開シンポジウム
  • Place of Presentation: 大阪
  • Year and Date: 2008-11-11
• [Presentation] 蛋白質の運動と連動する水和水のコヒーレントな集団運動の探索(招待講演) (2008)
  • Author(s): 中迫雅由
  • Organizer: 特定領域「高次系分子科学」第二回公開シンポジウム
  • Place of Presentation: 大阪大学
  • Year and Date: 2008-11-11
• [Presentation] データベース解析に基づく蛋白質の水和構造予測 (2008)
  • Author(s): 松岳大輔, 中迫雅由
  • Organizer: 特定領域「高次系分子科学」第二回公開シンポジウム
  • Place of Presentation: 大阪大学
  • Year and Date: 2008-11-11
• [Presentation] 蛋白質の運動と連動する水和水のコヒーレントな集団運動の探索 (2008)
  • Author(s): 中迫雅由
  • Organizer: 特定領域「高次系分子科学」第二回公開シンポジウム
  • Place of Presentation: 大阪大学
  • Year and Date: 2008-11-11
• [Presentation] Structural basis for the enantioselective decarboxylation by arylmalonate decarboxylase (2008)
  • Author(s): Rika Obata, Masayoshi Nakasako, Kenji Miyamoto and Hiromichi Ohta
  • Organizer: XXI Congress of the International Union of Crystallography
  • Place of Presentation: Osaka
  • Year and Date: 2008-08-27
• [Presentation] “Structural basis for the enantioselective decarboxylation by arylmalonate decarboxylase (2008)
  • Author(s): Rika Obata, Masayoshi Nakasako, K enji Miyamoto, Hiromichi Ohta
  • Organizer: XXI Congress of the International Union of Crystallography
  • Place of Presentation: Osaka, Japan
  • Year and Date: 2008-08-27
• [Presentation] Prediction of hydration structures around polar protein atoms through a data-base analysis (2008)
  • Author(s): Daisuke Matsuoka, Masayoshi Nakasako
  • Organizer: XXI Congress of the International Union of Crystallography
  • Place of Presentation: Osaka
  • Year and Date: 2008-08-25
• [Presentation] Prediction of hydration structures around polar protein atoms through a data-base analysis (2008)
  • Author(s): Daisuke Matsuoka, Masayoshi Nakasako
  • Organizer: XXI Congress of the International Union of Crystallography
  • Place of Presentation: Osaka, Japan
  • Year and Date: 2008-08-25
• [Presentation] Hydration structure changes around proteins at work (2008)
  • Author(s): Masayoshi Nakasako, Tsunero Sato and Mitsunori Ikeguchi
  • Organizer: XXI Congress of the International Union of Crystallography
  • Place of Presentation: Osaka(責任著者)
  • Year and Date: 2008-08-24
• [Presentation] Hydration structure changes around proteins at work (Invited Talk) (2008)
  • Author(s): Masayoshi Nakasako Mitsunori Ikeguchi
  • Organizer: XXI Congress of the International Union of Crystallography
  • Place of Presentation: Osaka, Japan
  • Year and Date: 2008-08-24
• [Presentation] データベース解析から予測される膜蛋白質の膜貫通領域における水和構造 (2008)
  • Author(s): 松岳大輔、中迫雅由
  • Organizer: 特定領域「高次系分子科学」ミニ公開シンポジウム「プロトンポンプを考える」
  • Place of Presentation: 大阪
  • Year and Date: 2008-08-06
• [Presentation] データベース解析から予測される膜蛋白質の膜貫通領域における水和構造(招待講演) (2008)
  • Author(s): 松岳大輔, 中迫雅由
  • Organizer: 特定領域「高次系分子科学」ミニ公開シンポジウム「プロトンポンプを考える」
  • Place of Presentation: 大阪大学
  • Year and Date: 2008-08-06
• [Presentation] How blue light regulates kinase activity of phototropin (2008)
  • Author(s): Satoru Tokutomi, Daisuke Matsuoka, Kazunori zikihara, Koji Okajima, Hitomi Katsura, Shizue Yoshihara, Masayoshi Nakasako
  • Organizer: 34th American Society for Photobiology Meeting
  • Place of Presentation: California
  • Year and Date: 2008-06-23
• [Presentation] タンパク質の水和構造を探る (2008)
  • Author(s): 中迫雅由
  • Organizer: 東京工業大学資源化学研究所セミナー
  • Place of Presentation: 横浜
  • Year and Date: 2008-06-13
• [Presentation] タンパク質の水和構造を探る (2008)
  • Author(s): 中迫雅由
  • Organizer: 東京工業大学 資源化学研究所セミナー
  • Place of Presentation: 東京工業大学(長津田)
  • Year and Date: 2008-06-13
• [Presentation] データベース解析によるタンパク質の水和構造予測 (2008)
  • Author(s): 松岳大輔,中迫雅由
  • Organizer: 第8 回日本蛋白質科学会
  • Place of Presentation: 東京
  • Year and Date: 2008-06-10
• [Presentation] データベース解析によるタンパク質の水和構造予測 (2008)
  • Author(s): 松岳大輔, 中迫雅由
  • Organizer: 第8回日本蛋白質科学会
  • Place of Presentation: 東京
  • Year and Date: 2008-06-10
• [Presentation] 蛋白質の運動と連動する水和水のコヒーレントな集団運動の探索 (2008)
  • Author(s): 中迫雅由
  • Organizer: 特定領域「高次系分子科学」合同班会議
  • Place of Presentation: 新潟
  • Year and Date: 2008-05-27
• [Presentation] Crystal structures of LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana (2008)
  • Author(s): Masayoshi Nakasako, Daisuke, Matsuoka, Kazunori Zikihara, Hitomi Katsura and Satoru Tokutomi
  • Organizer: The 5-th open workshop "Chemistry of Biological Processes Created by Water and Biomolecules
  • Place of Presentation: Nara
  • Year and Date: 2008-01-24
• [Presentation] Crystal structure of arylmalonate decarboxylase (2008)
  • Author(s): Masayoshi Nakasako, Rika Obata, Kenji Miyamoto and Hiromichi Ohta
  • Organizer: The 5-th open workshop "Chemistry of Biological Processes Created by Water and Biomolecules
  • Place of Presentation: Nara
  • Year and Date: 2008-01-24
• [Presentation] Search for determinants regulating the quaternary structures of Fvfragments of antibodies through a database analysis (2008)
  • Author(s): Masashi Miyazawa, Masayoshi Nakasako
  • Organizer: The 5-th open workshop "Chemistry of Biological Processes Created by Water and Biomolecules
  • Place of Presentation: Nara
  • Year and Date: 2008-01-24
• [Presentation] Surface structure of glutamate dehydrogenase crystal observed by atomic force microscopy (2008)
  • Author(s): Tsuneo Sato, Masayoshi Nakasako
  • Organizer: The 5-th open workshop "Chemistry of Biological Processes Created by Water and Biomolecules
  • Place of Presentation: Nara
  • Year and Date: 2008-01-24
• [Presentation] How blue light regulates kinase activity of phototropin (Invited Talk) (2008)
  • Author(s): Satoru Tokutomi, Daisuke Matsuoka, Kazunori zikihara, Koji Okajima, Hitomi Katsura, Shizue Yoshihara, Masavoshi Nakasako
  • Organizer: 34th American Society for Photobiology Meeting
  • Place of Presentation: California, USA
• [Presentation] Observation of the surface of glutamate dehydrogenase crystals by atomic force microscopy (2007)
  • Author(s): Tsuneo Sato, Masayoshi Nakasako
  • Organizer: 日本生物物理学会第45 回年会
  • Place of Presentation: 横浜
  • Year and Date: 2007-12-23
• [Presentation] Crystal structures of LOV1 domains in Arabidopsis phototropin 1 and 2 (2007)
  • Author(s): Masayoshi Nakasako, Daisuke, Matsuoka, Kazunori Zikihara, Hitomi Katsura and Satoru Tokutomi
  • Organizer: 日本生物物理学会第45 回年会
  • Place of Presentation: 横浜
  • Year and Date: 2007-12-23
• [Presentation] Prediction of Hydration Structures around polar protein atoms through a data-base analysis (2007)
  • Author(s): Daisuke Matsuoka, Masayoshi Nakasako
  • Organizer: 日本生物物理学会第45 回年会
  • Place of Presentation: 横浜
  • Year and Date: 2007-12-23
• [Presentation] Search for determinants regulating the quaternary structures of Fvfragments of antibodies through a database analysis (2007)
  • Author(s): Miyazawa Masashi, Masayoshi Nakasako
  • Organizer: 日本生物物理学会第45 回年会
  • Place of Presentation: 横浜
  • Year and Date: 2007-12-23
• [Presentation] Simulation on the X-ray speckle patterns of a hydrated protein molecule with conformational variations (2007)
  • Author(s): Keita Sakamoto, Mitsunori Ikeguchi, Masayoshi Nakasako
  • Organizer: 日本生物物理学会第45 回年会
  • Place of Presentation: 横浜
  • Year and Date: 2007-12-23
• [Presentation] Simulation on the X-ray speckle patterns of a hydrated protein molecule with conformational variations (2007)
  • Author(s): Sakamoto Keita, Ikeguchi Mitsunori, Nakasako Masayoshi
  • Organizer: 日本生物物理学会第45回年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2007-12-23
• [Presentation] Search fbr determinants regulating the quatemary structures of Fv ffagments of antibodies through a database analysis (2007)
  • Author(s): Miyazawa Masashi and Nakasako Masayoshi
  • Organizer: 日本生物物理学会第45回年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2007-12-23
• [Presentation] Prediction of Hydration Structures around polar protein atoms through a data-base analysis (2007)
  • Author(s): Matsuoka Daisuke and Nakasako Masayoshi
  • Organizer: 日本生物物理学会第45回年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2007-12-23
• [Presentation] Clystal structures of LOV1 domains in Arabidopsis phototropin 1 and 2 (2007)
  • Author(s): Masayoshi Nakasako, Daisuke, Matsuoka, Kazunori Zikihara, Hitomi Katsura and Satoru Tokutomi
  • Organizer: 日本生物物理学会第45回年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2007-12-23
• [Presentation] Observation of the surface of glutamate dehydrogenase crystals by atomic fbrce microscopy (2007)
  • Author(s): Sato Tsunero and Nakasako Masayoshi
  • Organizer: 日本生物物理学会第45回年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2007-12-23
• [Presentation] X線溶液散乱で何が分かるのか? なぜ放射光なのか? (2007)
  • Author(s): 中迫雅由
  • Organizer: 第2回X線溶液散乱研究会-SPring-8 における放射光X 線溶液散乱-
  • Place of Presentation: 播磨
  • Year and Date: 2007-10-11
• [Presentation] X線溶液散乱で何が分かるのか?なぜ放射光なのか? (2007)
  • Author(s): 中迫 雅由
  • Organizer: 第2回X線溶液散乱研究会-SPring-8における放射光X線溶液散乱-
  • Place of Presentation: 理化学研究所播磨研究所
  • Year and Date: 2007-10-11
• [Presentation] 蛋白質表面に吸着した水分子と蛋白質運動の相関について (2007)
  • Author(s): 中迫雅由
  • Organizer: 日本物理学会第62回年次大会
  • Place of Presentation: 札幌
  • Year and Date: 2007-09-23
• [Presentation] 蛋白質表面に吸着した水分子と蛋白質運動の相関について (2007)
  • Author(s): 中迫 雅由
  • Organizer: 日本物理学会第62回年次大会
  • Place of Presentation: 北海道大学
  • Year and Date: 2007-09-23
• [Presentation] Hydration structure changes around proteins at work (2007)
  • Author(s): Masayoshi Nakasako
  • Organizer: Third Japanese-French seminar on structural dynamics of proteins
  • Place of Presentation: Grenoble, France
  • Year and Date: 2007-01-18
• [Remarks]
  • URL: http://www.phys.keio.ac.jp/guidance/labs/nakasako/nakasako-lab.html