Innovative technological development for the production of the complex crystal with high-strength hydrogel

• Project/Area Number: 25286051
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Crystal engineering
• Research Institution: Osaka University
• Principal Investigator: SUGIYAMA SHIGERU 大阪大学, 理学(系)研究科(研究院), 准教授 (90615428)
• Co-Investigator(Renkei-kenkyūsha): MATSUMORI NOBUAKI 九州大学, 理学(系)研究科(研究院), 教授 (50314357) ; TERAI TAKUYA 東京大学, 薬学研究科(研究院), 助教 (00508145)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000); Fiscal Year 2015: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000); Fiscal Year 2014: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2013: ¥14,560,000 (Direct Cost: ¥11,200,000、Indirect Cost: ¥3,360,000)
• Keywords: 結晶工学 / 結晶成長 / 脂質結合タンパク質 / 凝固ゲル / 創薬スクリーニング / Ｘ線構造解析 / 脂質 / 難水溶性化合物 / 難水溶性 / 浸漬 / 脂肪酸 / タンパク質 / 固相ゲル / SBDD

Outline of Final Research Achievements

X-ray crystallography offers an unprecedented opportunity to facilitate drug discovery. The structural information of the protein-ligand complex has the potential to find ways to improve the lead compounds. The best way is to determine the three dimensional structure of the complex by soaking the ligand in crystals. However, the soaking step has a problem because many lead compounds are low water-soluble. Such lead compounds must be dissolved in concentrated organic solvents, such as dimethyl sulfoxide (DMSO). We recently developed a new method for growing crystals in a high-strength hydrogel. This method enabled us to increase the mechanical stability of the crystals. In this study, we transferred the hydrogel-grown avidin/streptavidin or FABP crystals into a 50% DMSO solution containing the inhibitors. We observed the clear electron density maps of the compounds that are bound to the active sites.

Research Products

• [Journal Article] Genetically engineered monomeric streptavidin for designing a new detection systems based on monovalent biotin interaction (2016)
  • Author(s): Osamu Hiraoka, Takuya Terai, Moe Kohno, Shigeru Sugiyama
  • Journal Title: The ShujitusUniversity Jounal of Pharmaceutical Sciences Volume: 3 Pages: 16-26
  • NAID: 120006535112
  • Peer Reviewed
• [Journal Article] Development of protein seed crystals reinforced by high-strength hydrogels (2015)
  • Author(s): Shigeru Sugiyama, Noriko Shimizu, Keisuke Kakinouchi, Osamu Hiraoka, Hiroyoshi Matsumura, Hiroshi Y. Yoshikawa, Yoshinori Takahashi, Mihoko Maruyama, Masashi Yoshimura, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Tsuyoshi Inoue, Michio Murata, and Yusuke Mori
  • Journal Title: CrystEngComm Volume: 17 Issue: 42 Pages: 8064-8071
  • DOI: 10.1039/c5ce00844a
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport (2015)
  • Author(s): Takuya Terai, Moe Kohno, Gaelle Boncompain, Shigeru Sugiyama, Nae Saito, Ryo Fujikake, Tasuku Ueno, Toru Komatsu, Kenjiro Hanaoka, Takayoshi Okabe, Yasuteru Urano, Franck Perez, and Tetsuo Nagano
  • Journal Title: J. Am. Chem. Soc. Volume: 137 Issue: 33 Pages: 10464-10467
  • DOI: 10.1021/jacs.5b05672
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Bioactive Structure of Membrane Lipids and Natural Products Elucidated by a Chemistry-Based Approach (2015)
  • Author(s): Murata, M; Sugiyama, S; Matsuoka, S; Matsumori, N
  • Journal Title: Chemical Record Volume: 15 Issue: 4 Pages: 675-690
  • DOI: 10.1002/tcr.201402097
  • Peer Reviewed
• [Journal Article] A comparative analysis of microgravity and earth grown thermostable T1 Lipase crystals using HDPCG apparatu (2015)
  • Author(s): Raja Noor Zaliha Raja Abd Rahman, Mohd. Shukuri Mohamad Ali, Shigeru Sugiyama, Adam Thean Chor Leow, Tsuyoshi Inoue, Mahiran Basri, Abu Bakar Salleh, and Hiroyoshi Matsumura
  • Journal Title: Protein Pept. Lett Volume: 22 Issue: 2 Pages: 173-179
  • DOI: 10.2174/0929866521666141019193604
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Preliminary X-ray analysis of the binding domain of the soybean vacuolar sorting receptor complexed with a sorting determinant of a seed storage protein. (2015)
  • Author(s): Maruyama, N., Goshi, T., Sugiyama, S., Niiyama, M., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Matsumura, H., Mikami, B.
  • Journal Title: Acta Crystallogr. F Struct. Biol. Commun. Volume: 71 Issue: 2 Pages: 132-135
  • DOI: 10.1107/s2053230x14027484
  • Peer Reviewed / Open Access
• [Journal Article] Molecular Dynamics Simulations of Heart-type Fatty Acid-binding Protein in Apo and Holo Forms, and Hydration Structure Analyses in the Binding Cavity. (2015)
  • Author(s): Daisuke Matsuoka, Shigeru Sugiyama, Michio Murata, Shigeru Matsuoka*
  • Journal Title: J. Phys. Chem. B Volume: 119 Issue: 1 Pages: 114-127
  • DOI: 10.1021/jp510384f
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Water-mediated recognition of simple alkyl chains by heart-ype fatty acid-binding protein. (2015)
  • Author(s): Shigeru Matsuoka, Shigeru Sugiyama, Daisuke Matsuoka, Mika Hirose, Sebastien Lethu, Hikaru Ano, Toshiaki Hara, Osamu Ichihara, S. Roy Kimura, Satoshi Murakami, Hanako Ishida, Eiichi Mizohata, Tsuyoshi Inoue, Michio Murata
  • Journal Title: Angew. Chem. Int. Ed. Volume: 54 Issue: 5 Pages: 1508-1511
  • DOI: 10.1002/anie.201409830
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Anion Order-to-Disorder Transition in Layered Iron Oxyfluoride Sr2FeO3F Single Crystals (2014)
  • Author(s): Y. Tsujimoto, Y. Matsushita, N. Hayashi, K. Yamaura, and T. Uchikoshi
  • Journal Title: Crystal Growth & Design Volume: 14 Issue: 9 Pages: 4278-4284
  • DOI: 10.1021/cg500484e
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Crystallization and preliminary crystallographic studies of PotA, a membrane-associated ATPase of the spermidine-preferential uptake system in Thermotoga maritime. (2014)
  • Author(s): Sugiyama, S. et al.
  • Journal Title: Acta Crystallogr. F Struct. Biol. Commun. Volume: 70 Issue: 6 Pages: 738-741
  • DOI: 10.1107/s2053230x14008607
  • Peer Reviewed
• [Journal Article] Interaction kinetics of liposome-incorporated unsaturated fatty acids with fatty acid-binding protein 3 by surface plasmon resonance (2014)
  • Author(s): Maria Carmen Tan, Shigeru Matsuoka, Hikaru Ano, Hanako Ishida, Mika Hirose, Fuminori Sato, Shigeru Sugiyama, Michio Murata
  • Journal Title: Bioorganic & Medicinal Chemistry Volume: 22 Issue: 6 Pages: 1804-8
  • DOI: 10.1016/j.bmc.2014.02.001
  • Peer Reviewed
• [Journal Article] A novel approach for protein crystallization by a synthetic hydrogel with thermoreversible gelation polymer (2013)
  • Author(s): S. Sugiyama, N. Shimizu, G. Sazaki, M. Hirose, Y. Takahashi, M. Maruyama, H. Matsumura, H. Adachi, K. Takano, S. Murakami, T. Inoue, and Y. Mori,
  • Journal Title: Cryst. Growth Des. Volume: 13 Issue: 5 Pages: 1899-1904
  • DOI: 10.1021/cg301588b
  • Peer Reviewed
• [Journal Article] Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilinonaphthalene-8-sulphonic acid (2013)
  • Author(s): Mika Hirose, Shigeru Sugiyama, Hanako Ishida, Mayumi Niiyama, Daisuke Matsuoka, Toshiaki Hara, Eiichi Mizohata, Satoshi Murakami,
  • Journal Title: J. Synchrotron Rad. Volume: 20 Issue: 6 Pages: 923-8
  • DOI: 10.1107/s0909049513021298
  • Peer Reviewed
• [Journal Article] 溶液流れ下におけるタンパク質の結晶成長 (2013)
  • Author(s): 丸山美帆子、佐﨑元、高橋義典、吉村政志、吉川洋史、杉山成、安達宏昭、松村浩由、井上豪、高野和文、村上聡、森勇介
  • Journal Title: 日本結晶成長学会誌 Volume: 40 Pages: 72-82
  • Peer Reviewed
• [Presentation] フェムト秒レーザーアブレーションを用いた成長機構転換によるタンパク質結晶の高品質化 (2016)
  • Author(s): 冨永勇佑、丸山美帆子、吉村政志、杉山成、安達宏昭、塚本勝男、松村浩由、高野和文、村上聡、井上豪、吉川洋史、森勇介
  • Organizer: 第63回応用物理学会春季学術講演会
  • Place of Presentation: 東京工業大学大岡山キャンパス（東京）
  • Year and Date: 2016-03-19
  • Invited
• [Presentation] Growth of Protein Crystals in High-Strength Hydrogels (2015)
  • Author(s): S. Sugiyama
  • Organizer: 3rd International Picobiology Institute Symposium
  • Place of Presentation: Center for Advanced Science and Technology (CAST)
  • Year and Date: 2015-12-08
  • Int'l Joint Research / Invited
• [Presentation] L-アミノ酸酸化酵素の構造に基づく基質認識機構と反応特異性 (2015)
  • Author(s): 伊藤菜奈子、浅田貴大、村上佳穂、杉山成、川口辰也、赤地周作、北野量、田村隆、稲垣賢二、今田勝巳
  • Organizer: 第38回日本分子生物学会年会・第88回日本生化学会大会合同大会（BMB2015）
  • Place of Presentation: 神戸ポートピアホテル
  • Year and Date: 2015-12-01
• [Presentation] 創薬スクリーニングに向けた難溶性化合物との複合体結晶作製技術 (2015)
  • Author(s): 杉山成・垣之内啓介・高野和文・松村浩由・安達宏昭・丸山美帆子・吉川洋史・高橋義典・吉村政志・村上聡・井上豪・村田道雄・森勇介
  • Organizer: 第45回結晶成長国内会議（NCCG-45）
  • Place of Presentation: 北海道大学学術交流会館
  • Year and Date: 2015-10-19
• [Presentation] ゲル化タンパク質溶液へ撹拌操作による結晶核発生数の制御 (2015)
  • Author(s): 丸山美帆子，林佑紀，吉川洋史，岡田詩乃，杉山成，小泉晴比古，橘勝，安達宏昭，松村浩由，井上豪，高野和文，村上聡，吉村政志，森勇介
  • Organizer: 第45回結晶成長国内会議（NCCG-45）
  • Place of Presentation: 北海道大学学術交流会館
  • Year and Date: 2015-10-19
• [Presentation] ゲル化タンパク質溶液へのフェムト秒レーザー集光による核発生の空間制御 (2015)
  • Author(s): 山形眞，丸山美帆子，冨永勇佑，吉川洋史，杉山成，岡田詩乃，高橋義典，安達宏昭，高野和文，村上聡，井上豪，松村浩由，吉村政志，森勇介
  • Organizer: 第45回結晶成長国内会議（NCCG-45）
  • Place of Presentation: 北海道大学学術交流会館
  • Year and Date: 2015-10-19
• [Presentation] 広範な結晶化条件に適応した新規凝固ゲル中結晶化法 (2015)
  • Author(s): 垣之内啓介, 高野和文, 村上聡, 安達宏昭, 丸山美帆子, 吉川洋史, 高橋義典, 吉村政志, 松村浩由, 井上豪, 村田道雄, 森勇介, 杉山成
  • Organizer: 平成27年度日本結晶学会年会
  • Place of Presentation: 大阪府立大学
  • Year and Date: 2015-10-17
• [Presentation] 創薬加速に向けた難溶性低分子複合体結晶作製の革新的技術開発 (2015)
  • Author(s): 杉山成、垣之内啓介・石田英子・松村浩由・安達宏昭・高野和文・丸山美帆子・吉川洋史・高橋義典・吉村政志・村上聡・井上豪・村田道雄・森勇介
  • Organizer: 第64回高分子討論会
  • Place of Presentation: 山形県仙台市 東北大学川内キャンパス
  • Year and Date: 2015-09-15
• [Presentation] 膜蛋白質－膜脂質の相互作用解析を目指した重元素化脂質の利用 (2015)
  • Author(s): 杉山成
  • Organizer: 第53回日本生物物理学会年会シンポジウム
  • Place of Presentation: 金沢大学角間キャンパス（石川県、金沢市）
  • Year and Date: 2015-09-13
  • Invited
• [Presentation] ゲル化タンパク溶液におけるフェムト秒レーザー誘起核発生の空間制御 (2015)
  • Author(s): 山形眞，丸山美帆子，冨永勇佑，吉川洋史，杉山成，岡田詩乃，高橋義典，安達宏昭，高野和文，村上聡，井上豪，松村浩由，吉村政志，森勇介
  • Organizer: ゲル化タンパク溶液におけるフェムト秒レーザー誘起核発生の空間制御
  • Place of Presentation: 名古屋国際会議場（愛知)
  • Year and Date: 2015-09-13
• [Presentation] 難溶性化合物とタンパク質との相互作用解析へ向けた新規技術開発 (2015)
  • Author(s): 杉山成, 垣之内啓介, 松村浩由, 安達宏昭, 高野和文, 丸山美帆子, 高橋義典, 吉川洋, 吉村政志, 村上聡, 井上豪, 村田道雄, 森勇介
  • Organizer: 第53回日本生物物理学会年会
  • Place of Presentation: 石川県金沢市 金沢大学角間キャンパス
  • Year and Date: 2015-09-13
• [Presentation] 難溶性化合物とタンパク質との複合体結晶解析へ向けた新しい取り組み (2015)
  • Author(s): 杉山成
  • Organizer: 大阪大学蛋白研セミナー
  • Place of Presentation: 大阪大学蛋白質研究所 1階講堂（大阪）
  • Year and Date: 2015-08-27
  • Invited
• [Presentation] SPIRAL GROWTH OF PROTEIN CRYSTALS INDUCED BY FEMTOSECOND LASER ABLATION (2015)
  • Author(s): Y. Tominaga, M. Maruyama, H. Yoshikawa, Y. Hayashi, S. Nakayama, Y. Takahashi, S. Sugiyama, H. Adachi, H. Matsumura, K. Takano, S. Murakami, T. Inoue, M. Yoshimura, Y. Mori
  • Organizer: 20th American Conference on Crystal Growth and Epitaxy (ACCGE-20)
  • Place of Presentation: Big Sky, Montana, USA
  • Year and Date: 2015-08-02
  • Int'l Joint Research
• [Presentation] Protein crystallization with increased mechanical stability by using a semi-solid hydrogel combined with the stirring technique (2015)
  • Author(s): M. Maruyama, Y. Hayashi, M. Yoshimura, H. Y. Yoshikawa, S. Okada, S. Sugiyama, H. Adachi, H. Matsumura, T. Inoue, K. Takano, S. Murakami, and Y. Mori
  • Organizer: 20th American Conference on Crystal Growth and Epitaxy (ACCGE-20)
  • Place of Presentation: Big Sky, Montana, USA
  • Year and Date: 2015-08-02
  • Int'l Joint Research
• [Presentation] L-リシン酸化酵素基質複合体の結晶構造 (2015)
  • Author(s): 近藤裕輝, 伊藤菜々子, 杉山成, 川口辰也, 天野万里, 新屋敷健悟, 日下部均, 田村隆, 稲垣賢二, 今田勝巳
  • Organizer: 第15回蛋白質科学会年会
  • Place of Presentation: 徳島市あわぎんホール
  • Year and Date: 2015-06-24
• [Presentation] 広範な結晶化条件に適応した新規凝固ゲル中結晶化法 (2015)
  • Author(s): 垣之内啓介, 高野和文, 村上聡, 安達宏昭, 丸山美帆子, 吉川洋史, 高橋義典, 吉村政志, 松村浩由, 井上豪, 村田道雄, 森勇介, 杉山成
  • Organizer: 第15回蛋白質科学会年会
  • Place of Presentation: 徳島市あわぎんホール
  • Year and Date: 2015-06-24
• [Presentation] タンパク質の脂質認識機構と脂溶性化合物を扱うための技術開発 (2015)
  • Author(s): 杉山成
  • Organizer: 第27回鴨叡会・生命分子化学科セミナー
  • Place of Presentation: 京都府立大学
  • Year and Date: 2015-01-27
  • Invited
• [Presentation] A Novel Approach for Protein Crystallization with High-strength Hydrogels (2014)
  • Author(s): Shigeru Sugiyama
  • Organizer: The Collaborative Conference on Crystal Growth 2014 (3CG2014)
  • Place of Presentation: Phuket, Thailand
  • Year and Date: 2014-11-04 – 2014-11-07
  • Invited
• [Presentation] ゲルを利用したタンパク質結晶化法 (2014)
  • Author(s): 杉山成
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 札幌
  • Year and Date: 2014-09-25 – 2014-09-27
  • Invited
• [Presentation] Hydrogel Protects Protein Crystals From Osmotic Shock (2014)
  • Author(s): Shigeru Sugiyama
  • Organizer: 15th International Conference on the Crystallization of Biological Macromolecules (ICCBM15)
  • Place of Presentation: Hamburg, Germany
  • Year and Date: 2014-09-17 – 2014-09-20
  • Invited
• [Presentation] ゲルを利用したタンパク質結晶化法 (2014)
  • Author(s): 杉山成
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Invited
• [Presentation] 固相ハイドロゲル中でのタンパク質の結晶化 (2014)
  • Author(s): 杉山成
  • Organizer: 日本物理学会第69回年次大会
  • Place of Presentation: 東海大学 湘南キャンパス
  • Invited
• [Presentation] 固相ゲル結晶化法 (2013)
  • Author(s): 杉山成
  • Organizer: （独）日本学術振興会、回折構造生物第169委員会、第43回研究会
  • Place of Presentation: 東京 ゆうぽうと
  • Invited
• [Presentation] A New Approach for Protein Crystallization by Mebiol Hydrogel with Thermoreversible Gelation Polymer (2013)
  • Author(s): S. Sugiyama, N. Shimizu, G. Sazaki, M. Hirose, Y. Takahashi, M. Maruyama, H. Matsumura, H. Adachi, K. Takano, S. Murakami, T. Inoue, and Y. Mori
  • Organizer: The International Conference on Structural Genomics 2013 (ICSG2013)
  • Place of Presentation: Sapporo, KEIO PLAZA hotel
• [Presentation] Structure of the human muscle fatty acid-binding protein complexed with competitive inhibitor (2013)
  • Author(s): M. Hirose, S. Sugiyama, H. Ishida, D. Matsuoka, T. Hara, E. Mizohata, T. Inoue, S. Matsuoka, M. Murata
  • Organizer: The International Conference on Structural Genomics 2013 (ICSG2013)
  • Place of Presentation: Sapporo, KEIO PLAZA hotel
• [Presentation] Structure of the human muscle fatty acid-binding protein complexed with Hydrophobic ligand (2013)
  • Author(s): M. Hirose, S. Sugiyama, H.o Ishida, D. Matsuoka, T. Hara, E. Mizohata, T. Inoue, S. Matsuoka, M. Murata
  • Organizer: 4th International Symposium on Diffraction Structural Biology 2013 (ISDSB2013)
  • Place of Presentation: Nagoya Aichi, Japan
• [Presentation] 固相メビオールゲル中で育成させるタンパク質結晶化技術 (2013)
  • Author(s): 杉山成，清水典子，佐崎元，高橋義典，廣瀬未果，石田英子，丸山美帆子，松村浩由，安達宏昭，高野和文，村上聡，井上豪，森勇介
  • Organizer: 第43回結晶成長国内会議（NCCG-43）
  • Place of Presentation: 長野市生涯学習センター (TOiGO内)
• [Presentation] 脂肪酸結合タンパク質FABP3 の基質認識機構と機能 (2013)
  • Author(s): 松岡茂, 杉山成, 松岳大輔, 廣瀬未果, 新山真由美, 大塚康平, 村田道雄, 溝端栄一, 井上豪
  • Organizer: 第55回天然有機化合物討論会
  • Place of Presentation: 同志社大学
• [Presentation] 固相ハイドロゲルを利用したタンパク質結晶化技術の開発と応用 (2013)
  • Author(s): 杉山成、清水典子、佐﨑元、廣瀬未果、高橋義典、丸山美帆子、松村浩由、安達宏昭、高野和文、村上聡、井上豪、森勇介
  • Organizer: 第62回高分子討論会
  • Place of Presentation: 金沢大学 角間キャンパス
• [Presentation] 新規ストレプトアビジン可逆的結合分子の開発 (2013)
  • Author(s): 河野萌、寺井琢也、杉山成、岡部隆義、長野哲雄、花岡健二郎
  • Organizer: 日本ケミカルバイオロジー学会 第8回年会
  • Place of Presentation: 東京医科歯科大学
• [Book] ゲルテクノロジーハンドブック－機能設計・評価・シミュレーションから製造プロセス・製品化まで (2014)
  • Author(s): 監修：中野義夫
  • Total Pages: 835
  • Publisher: 株式会社エヌ・ティー・エス
• [Book] タンパク質結晶の最前線 (2013)
  • Author(s): 杉山成
  • Total Pages: 288
  • Publisher: 株式会社シーエムシー出版
• [Patent(Industrial Property Rights)] 重原子化化合物、膜タンパク質の結晶化を促進するための組成物、および該組成物を用いた膜タンパク質の構造解析方法 (2016)
  • Inventor(s): 杉山成、花島慎弥、村田道雄、井上豪、斎木悠、島田真典、松森信明
  • Industrial Property Rights Holder: 杉山成、花島慎弥、村田道雄、井上豪、斎木悠、島田真典、松森信明
  • Industrial Property Rights Type: 特許
  • Filing Date: 2016-03-29