Nature of chemical bond in biology including hydrogen and hydration.
| Project/Area Number |
17350080
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Chemistry related to living body
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| Research Institution | Ibaraki University |
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Principal Investigator |
NIIMURA Nobuo Ibaraki University, Graduate School of Science and Engineering, Professor (50004453)
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| Co-Investigator(Kenkyū-buntansha) |
TANAKA Ichiro Ibaraki University, College of Engineering, Assistant Professor (20354889)
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| Project Period (FY) |
2005 – 2007
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| Project Status |
Completed (Fiscal Year 2007)
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| Budget Amount *help |
¥14,170,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥570,000)
Fiscal Year 2007: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Fiscal Year 2006: ¥1,800,000 (Direct Cost: ¥1,800,000)
Fiscal Year 2005: ¥9,900,000 (Direct Cost: ¥9,900,000)
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| Keywords | neutron protein crystallography / structural biological chemistry / methyl group / confguration / mvoglobin / rubredoxin / hydrog+C601en bond / lone pair / エクリプス / スタガード / ニューマン投影 / 中性子回折 / 中性子構造生物 / 水素 / タンパク質 / ねじれ配座 / 重なり配座 / 中性子タンパク質構造解析 / 水和構造 / 双極子モーメント場 / 水素結合強度 / タンパク質化学結合 / タンパク質結晶成長 |
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| Research Abstract |
Methyl CH_3 group configuration
In gaseous ethane, C-C bond rotates freely but a staggered conformation is most stable and an eclipsed conformation is most unstable. Our high-resolution neutron diffraction analyses of myoglobin and other proteins have provided this information. The hydrogen atoms of alanine and isoleucine in rubredoxin are clearly identified. All the CH_3 group configurations in amino acid residues are extracted and discussed. It is found that most of the CH_3 groups belong to the stable staggered conformations (angles close to 60°), but several % of them appear to have values close to eclipsed conformations (defined by angles close to 0°).
Non-linear hydrogen bonds
In the neutron analysis of the α-helices of myoglobin, the linearity of the X-H…Y hydrogen bonds has been analyzed. The statistics of hydrogen bonds N-H…O=C of the α-helices of myoglobin have been obtained, where the length between H and O is r and the NHO and COH angles are θ_1, and θ_2, respectively. The non-linearity of the actual N-H…O bond angle θ_1 is correlated to the deviation of H…O=C angles θ_2 from the value of 120° normally expected for the lone pair electrons of an sp^2-hydridized carbonyl oxygen. It seems that the steric constraints imposed by the packing of atoms in a protein molecule, in this case an α-helix, necessitates considerable deviation normally found in small-molecule structures.
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Report
(4 results)
Research Products
(105 results)
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[Journal Article] Structural Refinement and Extraction of Hydrogen Atomic Positions in Polyoxymethylene Crystal Based on the First Successful Measurements of 2-Dimensional High-Energy Synchrotron X-ray Diffraction and Wide-Angle Neutron Diffraction Patterns of Hydrogenated and deuterated Species2007
Author(s)
Kohji, Tashiro・Makoto, Hanesaka・Takashi, Ohhara・Tomoji, Ozeki・Toshiaki, Kitano・Takashi, Nishu・Kazuo, Kurihara・Taro, Tamada・Ryota, Kuroki・Satoru, Fujiwara・Ichiro, Tanaka・Nobuo, Niimura, Ichi
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Journal Title
Polymer Journal 39
Pages: 1253-1273
NAID
Description
「研究成果報告書概要(和文)」より
Related Report
Peer Reviewed
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[Journal Article] Peak overlapping and its de-convolution in TOF diffraction data from neutron biological diffractometer in J-PARC2006
Author(s)
K., Kusaka・ T, ohhara・I, Tanaka・N, Niimura・T, Ozeki・K, Kurihara・K, Aizawa・Y, Morii・M, Arai・K, Ebata・Y, Takano
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Journal Title
Physica B 385-386
Pages: 1062-1065
Description
「研究成果報告書概要(和文)」より
Related Report
Peer Reviewed
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[Journal Article] Peak overlapping and its de-convolution in TOF diffraction data from neutron biological diffractometer in J-PARC2006
Author(s)
K. Kusaka, T. Ohhara, I. Tanaka, N. Niimura, T. Ozeki, K. Kurihara, K. Aizawa, Y. Morii, M. Arai, K. Ebata, Y. Takano
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Journal Title
Physica B 385-386
Pages: 1062-1062
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Neutron Biological Diffractometer in J-PARC Proposed Ibaraki Prefectural Government2006
Author(s)
I.Tanaka, N.Niimura, T.Ozeki, T.Ohhara, K.Kurihara, K.Kusaka, Y.Morii, K.Aizawa, M.Arai, T.Kasao, K.Ebata, Y.Takano
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Journal Title
I CANS-XVII Proceedings LA-UR-3904, Vol.III,
Pages: 937-945
Related Report
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[Journal Article] Peak overlapping and its de-convolution in TOF diffraction data form neutron biological diffractometer in J-PARC2006
Author(s)
K.Kusaka, T.Ohhara, I.Tanaka, N.Niimura, T.Ozeki, K.Kurihara, K.Aizawa, Y.Morii, M.Arai, K.Ebata, Y.Takano
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Journal Title
Physica B 385-386
Pages: 1062-1065
Related Report
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[Journal Article] Hydrogen and Hydration in Proteins and Nucleic Acids. Neutro Diffraction from bio-macromolecules at JAERI2005
Author(s)
Niimura, N., Arai, S., Kurihara, K., Chatake, T., Tanaka, I., Bau, R.
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Journal Title
Hydrogen- Hydration sensitive structural biology ( KubaPro, Co.Ltd.),Eds., Nobuo Niimura, Hiroshi Mizuno, John Helliwell, Eric Westhof 1-1
Pages: 17-35
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[Presentation] A neutron crystallographic analysis of bovine Rnase A at pD6.22008
Author(s)
D., Yaghi・M., Yamashita・Y., Ohnishi・K., Kurihara・R., Kuroki・T., Yamada・T., Ishikawa・T., Chatake・I., Tanaka・N., Niimura
Organizer
第5回「水と生体分子」公開ワークショップ奈良
Place of Presentation
奈良
Year and Date
2008-03-06
Description
「研究成果報告書概要(和文)」より
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[Presentation] Current Status of IBARAKI Biological Crystal Diffractometer in J-PARC:General View2007
Author(s)
Takaaki, Hosoya・K., Kusaka・T., Ohhara・K., Kurihara・N., Niimura・I., Tanaka・T., Ozeki・K., AiZawa・M., Arai・Y., Morii・M., Hayashi・K., Ebataand・Y., Takano
Organizer
the Internatioanl Conference for Neutron and X-ray Scattering 2007(ICNX2007)
Place of Presentation
バンドン(インドネシア)
Description
「研究成果報告書概要(和文)」より
Related Report
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[Presentation] Current Status of IBARAKI Biological Crystal Diffractometer In J-PARC : General View2007
Author(s)
Takaaki Hosoya, K. Kusaka, T. Ohhara, K. Kurihara, N. Niimura, I. Tanaka, T. Ozeki, K. Aizawa, M. Arai, Y. Morii, M. Hayashi, K. Ebataand Y. Takano
Organizer
the International Conference for Neutron and X-ray Scattering 2007(ICNX2007)
Place of Presentation
Bandung(Indonesia)
Description
「研究成果報告書概要(欧文)」より
Related Report
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[Presentation] Current Status of IBARAKI Biological Crystal Diffractometer in J-PARC: General View2007
Author(s)
Takaaki Hosoya, K. Kusaka, T. Ohhara, K. Kurihara, N. Niimura, I. Tanaka, T. Ozeki, K. Aizawa, M. Arai, Y. Morii, M. Hayashi, K. Ebataand Y. Takano
Organizer
the Internatioanl Conference for Neutron and X-ray Scattering 2007 (ICNX2007)
Place of Presentation
インドネシア
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