Technological improvement for Neutron Crystallographic Analysis of Protein Structures

2009 Fiscal Year Final Research Report

• Project/Area Number: 19370046
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Japan Atomic Energy Agency
• Principal Investigator: KUROKI Ryota Japan Atomic Energy Agency, 量子ビーム応用研究部門, 研究主席 (30391246)
• Co-Investigator(Kenkyū-buntansha): TAMADA Taro 日本原子力研究会発機構, 量子ビーム応用研究部門, 研究副主幹 (50391248) ; ADACHI Motoyasu 日本原子力研究会発機構, 量子ビーム応用研究部門, 研究員 (60293958) ; KIDOKORO Shun-ichi 長岡技術科学大学, 工学部, 准教授 (80195320) ; SAITO Minoru 弘前大学, 理工学部, 教授 (60196011) ; UMINO Hisao 日本原子力研究会発機構, 量子ビーム応用研究部門, 研究員 (20399421) ; OHHARA Takashi 日本原子力研究会発機構, 量子ビーム応用研究部門, 研究副主幹 (60391249) ; OKAZAKI Nobuo 日本原子力研究会発機構, 量子ビーム応用研究部門, 研究員 (60391900) ; KURIHARA Kazuo 日本原子力研究会発機構, 量子ビーム応用研究部門, 研究副主幹 (50354890)
• Project Period (FY): 2007 – 2009
• Keywords: タンパク質 / 中性子解析 / 水和水 / 水素原子 / 結晶構造

Research Abstract

Neutron diffraction is a powerful probe for the observation of hydrogen atoms important for protein function in biomolecules. However, it is necessary to prepare relatively large crystals to obtain neutron diffraction data. By introducing mutations into the amino acids involved in crystal contacts, and developing crystallization techniques to periodically supplement protein into the crystal mother liquor, we succeeded in growing large crystals suitable for collecting neutron diffraction data and solved the structures of human immunodeficiency virus-1 protease and porcine pancreatic elastase.

Research Products

• [Journal Article] 中性子と放射光の相補的な利用による創薬標的タンパク質の立体構造解析 (2010)
  • Author(s): 黒木良太、玉田太郎、栗原和男、大原高志、安達基泰
  • Journal Title: 薬学雑誌 130巻 Pages: 657-664
  • Peer Reviewed
• [Journal Article] 中性子回折による蛋白質単結晶の構造解析 (2010)
  • Author(s): 栗原和男、岡崎伸生、黒木良太
  • Journal Title: Radioisotopes 59巻 Pages: 263-277
  • Peer Reviewed
• [Journal Article] 中性子を用いた創薬標的蛋白質の立体構造解析 (2010)
  • Author(s): 安達基泰、黒木良太
  • Journal Title: 蛋白質核酸酵素 55巻 Pages: 82-87
  • Peer Reviewed
• [Journal Article] 中性子構造解析および超高分解能X線構造解析によるエラスターゼの高度な機能解明 (2010)
  • Author(s): 玉田太郎、黒木良太、木下誉富、多田俊治
  • Journal Title: 日本結晶学会誌 52巻 Pages: 133-137
  • Peer Reviewed
• [Journal Article] タンパク質構造解析における中性子結晶学 (2010)
  • Author(s): 黒木良太
  • Journal Title: 日本結晶学会誌 52巻 Pages: 48-51
  • Peer Reviewed
• [Journal Article] Small-sized human immunodeficiency virus type-1 protease inhibitors containing allophenylnorstatine to explore the S2' pocket. (2009)
  • Author(s): Hidaka, K., Kimura, T., Abdel-Rahman, H.M., Nguyen, J.T., McDaniel, K.F., Kohlbrenner, W.E., Molla, A., Adachi, M., Tamada, T., Kuroki, R., Katsuki, N., Tanaka, Y., Matsumoto, H., Wang, J., Hayashi, Y., Kempf, D.J., Kiso, Y.
  • Journal Title: J Med Chem. 52(23) Pages: 7604-7617
  • Peer Reviewed
• [Journal Article] Engineering an improved crystal contact across a solvent-mediated interface of human fibroblast growth factor 1. (2009)
  • Author(s): Meher, A.K., Blaber, S.I., Lee, J., Honjo, E., Kuroki, R., Blaber, M.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun. 65 Pages: 1136-1140
  • Peer Reviewed
• [Journal Article] A neutron crystallographic analysis of T6 porcine insulin at 2. 1 A resolution. (2009)
  • Author(s): Iwai, W., Yamada, T., Kurihara, K., Ohnishi, Y., Kobayashi, Y., Tanaka, I., Takahashi, H., Kuroki, R., Tamada, T., Niimura, N.
  • Journal Title: Acta Crystallogr D Biol Crystallogr. 65 Pages: 1042-1050
  • Peer Reviewed
• [Journal Article] A neutron crystallographic analysis of phosphate-free ribonuclease A at 1. 7 A resolution. (2009)
  • Author(s): Yagi, D., Yamada, T., Kurihara, K., Ohnishi, Y., Yamashita, M., Tamada, T., Tanaka, I., Kuroki, R., Niimura, N.
  • Journal Title: Acta Crystallogr D Biol Crystallogr. 65 Pages: 892-899
• [Journal Article] Combined high-resolution neutron and X-ray analysis of inhibited elastase confirms the active-site oxyanion hole but rules against a low-barrier hydrogen bond. (2009)
  • Author(s): Tamada, T., Kinoshita, T., Kurihara, K., Adachi, M., Ohhara, T., Imai, K., Kuroki, R., Tada, T.
  • Journal Title: J Am Chem Soc. 131 Pages: 11033-11040
• [Journal Article] Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography. (2009)
  • Author(s): Adachi, M., Ohhara, T., Kurihara, K., Tamada, T., Honjo, E., Okazaki, N., Arai, S., Shoyama, Y., Kimura, K., Matsumura, H., Sugiyama, S., Adachi, H., Takano, K., Mori, Y., Hidaka, K., Kimura, T., Hayashi, Y., Kiso, Y., Kuroki, R.
  • Journal Title: Proc Natl Acad Sci USA. 106 Pages: 4641-4646
  • Peer Reviewed
• [Journal Article] Low-barrier hydrogen bond in photoactive yellow protein. (2009)
  • Author(s): Yamaguchi, S., Kamikubo, H., Kurihara, K., Kuroki, R., Niimura, N., Shimizu, N., Yamazaki, Y., Kataoka, M.
  • Journal Title: Proc Natl Acad Sci USA. 106 Pages: 440-444
  • Peer Reviewed
• [Journal Article] 中性子結晶構造解析 (2009)
  • Author(s): 栗原和男、黒木良太
  • Journal Title: 化学と生物 47巻 Pages: 868-873
  • Peer Reviewed
• [Journal Article] X線と中性子を利用して決定した創薬標的タンパク質の立体構造 (2009)
  • Author(s): 黒木良太
  • Journal Title: 日本結晶学会誌 51巻 Pages: 98-99
• [Journal Article] Crystallization and preliminary neutron diffraction studies of HIV-1 protease cocrystallized with inhibitor KNI-272. (2008)
  • Author(s): Matsumura, H., Adachi, M., Sugiyama, S., Okada, S., Yamakami, M., Tamada, T., Hidaka, K., Hayashi, Y., Kimura, T., Kiso, Y., Kitatani, T., Maki, S., Yoshikawa, H.Y., Adachi, H., Takano, K., Murakami, S., Inoue, T., Kuroki, R., Mori, Y.
  • Journal Title: Acta Crystallogr Sect F64 Pages: 1003-1006
  • Peer Reviewed
• [Journal Article] Mutagenesis of the crystal contact of acidic fibroblast growth factor. (2008)
  • Author(s): Honjo, E., Tamada, T., Adachi, M., Kuroki, R., Meher, A., Blaber, M.
  • Journal Title: J. Synchrotron Radiat. 15 Pages: 285-287
  • Peer Reviewed
• [Journal Article] A neutron crystallographic analysis of a cubic porcine insulin at pD 6. 6. (2008)
  • Author(s): Ishikawa, T., Chatake, T., Ohnishi Y., Tanaka, I., Kurihara, K., Kuroki, R., Niimura N.
  • Journal Title: Chemical Physics 343 Pages: 152-158
  • Peer Reviewed
• [Journal Article] Residue 134 determines the dimer-tetramer assembly of nucleoside diphosphate kinase from moderately halophilic bacteria. (2008)
  • Author(s): Tokunaga, H., Ishibashi, M., Arisaka, F., Arai, S., Kuroki, R., Arakawa, T., Tokunaga, M.
  • Journal Title: FEBS Lett. 582 Pages: 1049-1054
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction studies of polyketide synthase-1 (PKS-1) from Cannabis sativa. (2008)
  • Author(s): Taguchi, C., Taura, F., Tamada, T., Shoyama, Y., Shoyama, Y., Tanaka, H., Kuroki, R., Morimoto, S.
  • Journal Title: Acta Crystallogr. F64 Pages: 217-220
  • Peer Reviewed
• [Journal Article] Structural refinement and extraction of hydrogen atomic positions in polyoxymethylene crystal based on first successful measurements of 2-dimensinal high-energy synchrotron x-ray diffraction and wide-angle neutron diffraction pattern of hydrogenated and deuterated species. (2007)
  • Author(s): Tashiro, K., Hanesaka, M., Ohhara, T., Ozeki, T., Kitano, T., Nishu, T., Kurihara, K., Tamada, T., Kuroki, R., Fujiwara, S., Tanaka, I., Niimura N.
  • Journal Title: Polymer J. 39 Pages: 1253-1273
  • Peer Reviewed
• [Journal Article] Protonation states of buried histidine residues in human deoxyhemoglobin revealed by neutron crystallography. (2007)
  • Author(s): Chatake, T., Shibayama, N., Park, S.Y., Kurihara, K.., Tamada, T., Tanaka, I., Niimura, N., Kuroki, R., Morimoto, Y.
  • Journal Title: J. Am. Chem. Soc. 129 Pages: 14840-14841
  • Peer Reviewed
• [Journal Article] “Crystal Lattice Engineering"an approach to engineer protein crystal contacts by creating intermolecular symmetry: Crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines. (2007)
  • Author(s): Yamada, H., Tamada, T., Kosaka, M., Miyata, K., Fujiki, S., Tano, M., Moriya, M., Yamanishi, M., Honjo, E., Tada, H., Ino, T., Yamaguchi, H., Futami, J., Seno, M., Nomoto, M., Hirata, T., Yoshimura, M., Kuroki, R.
  • Journal Title: Protein Science 16 Pages: 1389-1397
  • Peer Reviewed
• [Journal Article] A Dinuclear Ni(μ-H)Ru Complex Derived from H2. (2007)
  • Author(s): Ogo, S., Kabe, R., Uehara, K., Kure, B., Nishimura, T., Menon, S.C., Harada, R., Fukuzumi, S., Higuchi, Y., Ohhara, T., Tamada, T., Kuroki, R.
  • Journal Title: Science 316 Pages: 585-587
  • Peer Reviewed
• [Journal Article] Crystallization of porcine pancreatic elastase and a preliminary neutron diffraction experiment. (2007)
  • Author(s): Kinoshita, T., Tamada, T., Imai, K., Kurihara, K., Ohhara, T., Tada, T., Kuroki, R.
  • Journal Title: Acta Cryst. F63 Pages: 315-317
  • Peer Reviewed
• [Presentation] Collaborative Use of X-ray and Neutron Diffraction for Investigation of Enzyme-Inhibitor Interaction (2009)
  • Author(s): Ryota Kuroki
  • Organizer: Taiwan-Japan Joint Seminar on Crystallography and IPR Seminar
  • Place of Presentation: 大阪大学・蛋白質研究所(大阪府吹田市)
  • Year and Date: 2009-12-07
• [Presentation] X線と中性子を用いた創薬標的タンパク質の立体構造解析 (2009)
  • Author(s): 黒木良太
  • Organizer: 「生体超分子構造」第6回公開シンポジウム
  • Place of Presentation: 千里ライフサイエンスセンター(大阪府豊中市)
  • Year and Date: 2009-12-01
• [Presentation] Structure of Enzyme-Inhibitor Complex by Neutron Crystallography (2009)
  • Author(s): Ryota Kuroki
  • Organizer: Neutrons in Biology
  • Place of Presentation: Santa Fe, AR (USA)
  • Year and Date: 2009-10-25
• [Presentation] 中性子と放射光の相補的な利用による創薬標的タンパク質の立体構造解析 (2009)
  • Author(s): 黒木良太
  • Organizer: 日本薬学会第129年会一般シンポジウムS-30、「創薬を目指す量子ビーム施設-放射光と中性子の有効利用-」
  • Place of Presentation: 京都国際会議場(京都)
  • Year and Date: 2009-03-27
• [Presentation] X線と中性子を用いて解析したヒト免疫不全ウイルスプロテアーゼ-阻害剤複合体の立体構造 (2008)
  • Author(s): 黒木良太
  • Organizer: 酵素工学研究会30周年記念シンポジウム
  • Place of Presentation: かずさアカデミアホール(千葉県木更津市)
  • Year and Date: 2008-11-13
• [Presentation] Structures of Drug-Target Proteins Determined by both X-ray and Neutron Diffraction (2008)
  • Author(s): Ryota Kuroki
  • Organizer: The 21st Congress of the International Union of Crystallography (IUCr2008)
  • Place of Presentation: Osaka International Convention Center. (Osaka)
  • Year and Date: 2008-08-25
• [Presentation] 医薬品作用の基本原理:タンパク質のかたちと分子認識 (2008)
  • Author(s): 黒木良太
  • Organizer: 九州大学薬学部公開講座
  • Place of Presentation: 福岡市
  • Year and Date: 2008-07-20
• [Presentation] X線と中性子を用いて観測した蛋白質や水和水の構造 (2008)
  • Author(s): 黒木良太
  • Organizer: 中性子と放射光の相補利用セミナー
  • Place of Presentation: 臨床研究情報センター(神戸市)
  • Year and Date: 2008-02-08
• [Presentation] 「X線と中性子を用いて観測した蛋白質水和水の熱力学的特徴 (2007)
  • Author(s): 黒木良太
  • Organizer: 日本生物物理学会シンポジウム、立体構造から生体分子間相互作用の熱力学へ
  • Place of Presentation: 横浜国際会議場(横浜市)
  • Year and Date: 2007-12-05
• [Book] 「医療関連酵素」、酵素利用技術体系(小宮山眞監修) (2010)
  • Author(s): 安達基泰、角南智子、黒木良太
  • Total Pages: 34-37
  • Publisher: エヌ・ティー・エス
• [Book] I-第6章「抗体を用いた結晶化」、タンパク質結晶の新展開(高野和文監修) (2008)
  • Author(s): 玉田太郎、新井栄揮、本庄栄二郎、黒木良太
  • Total Pages: 119-129
  • Publisher: シーエムシー出版
• [Book] II-第2章「中性子」、タンパク質結晶の新展開(高野和文監修) (2008)
  • Author(s): 大原高志、玉田太郎、栗原和男、黒木良太
  • Total Pages: 178-188
  • Publisher: シーエムシー出版
• [Book] 「組換えタンパク質の発現と精製のコツ」、タンパク質精製と取り扱いのコツ(森山達哉編) (2007)
  • Author(s): 本庄栄二郎、黒木良太
  • Total Pages: 136-139、155-174
  • Publisher: 羊土社
• [Book] 「中性子解析」, 生命科学のための機器分析ハンドブック(西村善文編) (2007)
  • Author(s): 黒木良太、安達基泰、栗原和男、玉田太郎
  • Total Pages: 210-215
  • Publisher: 羊土社
• [Patent(Industrial Property Rights)] 生体分子の大型結晶育成のための方法および装置 (2009)
  • Inventor(s): 新井栄揮、黒木良太
  • Industrial Property Rights Holder: 日本原子力研究開発機構
  • Industrial Property Number: 特許・特許出願第2009-157615号
  • Filing Date: 2009-07-02