Characterization of gas- and solution-phase structures of not crystallizable proteins

• Project/Area Number: 26505009
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: オミクス計測科学
• Research Institution: Yokohama City University
• Principal Investigator: AKASHI Satoko 横浜市立大学, 生命医科学研究科, 准教授 (10280728)
• Project Period (FY): 2014-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2014: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: 蛋白質 / 生体分子 / 分析科学 / 質量分析 / タンパク質 / 国際情報交換 / フランス

Outline of Final Research Achievements

The gas-phase and solution structures of not crystallizable proteins with intrinsically disordered regions were characterized by ion mobility mass spectrometry (IM-MS) in combination with small angle X-ray scattering (SAXS) analysis and molecular dynamics simulation (MD simulation). To analyze the structures　observed　in　the　ESI　mass　spectra,　computational　calculations　were performed for the canonical　nucleosome　core particle. To characterize the structure of nucleosome core particle with CG-rich DNA sequence, sample preparation was examined with 147 bp-DNA fragment.

Research Products

• [Int'l Joint Research] University of New South Wales(オーストラリア)
• [Int'l Joint Research] INSERM(フランス)
• [Int'l Joint Research] Univ. of New South Wales(オーストラリア)
• [Int'l Joint Research] POSTECH(韓国)
• [Journal Article] Structural analysis and taste evaluation of γ-glutamyl peptides comprising sulfur-containing amino acids (2018)
  • Author(s): Amino Yusuke、Wakabayashi Hidehiko、Akashi Satoko、Ishiwatari Yutaka
  • Journal Title: Biosci. Biotechnol. Biochem. Volume: 82 Issue: 3 Pages: 383-394
  • DOI: 10.1080/09168451.2018.1436433
  • Peer Reviewed
• [Journal Article] 3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy (2017)
  • Author(s): M.Nagae, S.K.Mishra, M.Neyazaki, R.Oi, A.Ikeda, N.Matsugaki, S.Akashi, H.Manya, M.Mizuno, H.Yagi, K.Kato, T.Senda, T.Endo, T.Nogi, and Y.Yamaguchi
  • Journal Title: Genes Cells Volume: - Issue: 4 Pages: 348-359
  • DOI: 10.1111/gtc.12480
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structure and assembly mechanisms of toxic human islet amyloid polypeptide oligomers associated with copper. (2016)
  • Author(s): Lee, S.J.C., Choi, T.S. Lee, J.W., Lee, H.J., Mun D.-G., Akashi, S., Lee, S.-W., Lim, M.H., Kim, H.I.
  • Journal Title: Chem. Sci. Volume: 7 Issue: 8 Pages: 5398-5406
  • DOI: 10.1039/c6sc00153j
  • NAID: 120006557137
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Effect of Charge on the Conformation of Highly Basic Peptides including the Tail Regions of Histone Proteins by Ion Mobility Mass Spectrometry. (2016)
  • Author(s): Akashi, S., Downard, K.M.
  • Journal Title: Anal. Bioanal. Chem. Volume: 408 Issue: 24 Pages: 6637-6648
  • DOI: 10.1007/s00216-016-9777-4
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] The C-terminal acidic domain of histone chaperone human NAP1 is an efficient binding-assistant for histone H2A-H2B but not H3-H4. (2016)
  • Author(s): Ohtomo, H., Akashi, S., Moriwaki, Y., Okuwaki, M., Osakabe, A., Nagata, K., Kurumizaka, H., Nishimura, Y.
  • Journal Title: Genes Cells Volume: 21 Issue: 3 Pages: 252-264
  • DOI: 10.1111/gtc.12339
  • NAID: 120007135590
  • Peer Reviewed / Open Access
• [Journal Article] Comprehensive Characterization of Relationship Between Higher-Order Structure and FcRn Binding Affinity of Stress-Exposed Monoclonal Antibodies. (2016)
  • Author(s): Tsuchida, D., Yamazaki, K, Akashi, S.
  • Journal Title: Pharm. Res. Volume: 33 Issue: 4 Pages: 994-1002
  • DOI: 10.1007/s11095-015-1845-5
  • Peer Reviewed
• [Journal Article] Charge-neutralization effect of the tail regions on the histone H2A/H2B dimer structure. (2015)
  • Author(s): Saikusa, K., Shimoyama, S., Asano, Y., Nagadoi, A., Sato, M., Kurumizaka, H., Nishimura, Y., and Akashi, S.
  • Journal Title: Protein Science Volume: - Issue: 8 Pages: 20-27
  • DOI: 10.1002/pro.2673
  • Peer Reviewed / Open Access
• [Journal Article] Mass spectrometric approach for characterizing the disordered tail regions of the histone H2A/H2B dimer. (2015)
  • Author(s): Saikusa, K., Nagadoi, A., Hara, K., Fuchigami, S., Kurumizaka, H., Nishimura, Y., and Akashi, S.
  • Journal Title: Anal. Chem. Volume: 87 Issue: 4 Pages: 2220-2227
  • DOI: 10.1021/ac503689w
  • Peer Reviewed / Open Access
• [Presentation] ネイティブ質量分析 -ヌクレオソームから生命現象をつかさどる金属の解析まで- (2018)
  • Author(s): 明石知子
  • Organizer: 日本化学会第98春季年会
• [Presentation] アセチル化に伴うヌクレオソームの構造変化の解析 (2017)
  • Author(s): 七種和美・新屋大貴・加藤大貴・畔上奈々子・長土居有隆・泉俊輔・西村善文・胡桃坂仁志・明石知子
  • Organizer: 日本化学会第97春季年会（2017）
  • Place of Presentation: 慶應義塾大学（神奈川県横浜市）
  • Year and Date: 2017-03-16
• [Presentation] ネイティブな状態を捕える質量分析の構造生物学での展開 (2017)
  • Author(s): 明石知子
  • Organizer: 2017年度生命科学系合同年次大会
• [Presentation] Structural and biochemical analysis of overlapping dinucleosome containing histone variants and histone modifications (2017)
  • Author(s): Wataru Kobayashi, Maya Aihara1, Daiki Kato, Masako Koyama, Kazumi Saikusa, Satoko Akashi, Rintaro Inoue, Masaaki Sugiyama, Hitoshi Kurumizak
  • Organizer: EMBO Conference “The Nucleosome: From Atoms to Genomes”
  • Int'l Joint Research
• [Presentation] 再構成したヌクレオソームのネイティブ質量分析 (2017)
  • Author(s): 明石知子
  • Organizer: 第17回日本蛋白質科学会年会
• [Presentation] ヌクレオソームコア粒子のESI-MSにおける電荷分布の解析 (2017)
  • Author(s): 前川怜奈、大橋和音、長土居有隆、明石知子
  • Organizer: 第65回質量分析総合討論会
• [Presentation] 不揮発性緩衝液で調製したタンパク質複合体のNative質量分析 (2017)
  • Author(s): 七種和美、加藤大貴、長土居有隆、胡桃坂仁志、明石知子
  • Organizer: 第65回質量分析総合討論会
• [Presentation] Behavior of Intrinsically Disordered Regions in Protein Complexes (2016)
  • Author(s): Kazumi Saikusa, Akihisa Osakabe, Yasushi Kawata, Hitoshi Kurumizaka, Satoko Akashi
  • Organizer: 21st International Conference on Mass Spectrometry
  • Place of Presentation: Metro Toronto Convention Centre (Toronto, Canada)
  • Year and Date: 2016-08-21
  • Int'l Joint Research / Invited
• [Presentation] タンパク質複合体の天然変性領域の構造への影響 (2016)
  • Author(s): 明石知子
  • Organizer: 第16回日本蛋白質科学会年会
  • Place of Presentation: 福岡国際会議場（福岡県福岡市）
  • Year and Date: 2016-06-07
  • Invited
• [Presentation] 高塩基性ペプチドのコンフォメーションと電荷の関係の解析 (2016)
  • Author(s): 明石知子、Kevin Downard
  • Organizer: 第64回質量分析総合討論会
  • Place of Presentation: ホテル阪急エキスポパーク（大阪府吹田市）
  • Year and Date: 2016-05-18
• [Presentation] 高塩基性ペプチドのイオンモビリティ質量分析 (2016)
  • Author(s): 明石知子
  • Organizer: 第6回イオン移動度研究会
  • Place of Presentation: 首都大学東京（東京都八王子市）
• [Presentation] Overlapping dinucleosomeの構造生物学的および物理化学的解析 (2015)
  • Author(s): 足立風水也、越阪部晃永、堀越直樹、有村泰宏、七種和美、明石知子、西村善文、杉山正明、河野秀俊、胡桃坂仁志
  • Organizer: 第38回日本分子生物学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2015-12-01
• [Presentation] Comprehensive Characterization of Relationship between Higher-Order Structure and Biological Function of Stress-Exposed Monoclonal Antibodies (2015)
  • Author(s): Daisuke Tsuchida, Katsuyoshi Yamazaki, Satoko Akashi
  • Organizer: Mass Spec 2015
  • Place of Presentation: Brooklyn (USA)
  • Year and Date: 2015-09-22
  • Int'l Joint Research
• [Presentation] Ion mobility mass spectrometry to investigate the stability of β-crystallin dimers to increased oxidation and its significance to RP-MS/protein footprinting applications (2015)
  • Author(s): Kevin Downard, Satoko Akashi, Simin Maleknia, Kazumi Saikusa
  • Organizer: 36th British Mass Spectrometry Society Annual Meeting
  • Place of Presentation: Birmingham (UK)
  • Year and Date: 2015-09-15
• [Presentation] Native Mass Spectrometry of Protein Complexes with Intrinsically Disordered Regions (2015)
  • Author(s): Satoko Akashi
  • Organizer: 2015 Korean Society for Mass Spectrometry Annual Meeting
  • Place of Presentation: Busan (Korea)
  • Year and Date: 2015-08-19
  • Invited
• [Presentation] Behavior of histone H2A/H2B dimers in the gas phase (2015)
  • Author(s): Satoko Akashi
  • Organizer: The 3rd Global Mass Spectrometry Trends and Ion Chemistry
  • Place of Presentation: Pohang (Korea)
  • Year and Date: 2015-08-17
  • Int'l Joint Research / Invited
• [Presentation] 水素／重水素交換－質量分析を用いたバイオ医薬品の構造活性相関の解析 (2015)
  • Author(s): 土田大介、山﨑勝由、明石知子
  • Organizer: 第63回質量分析総合討論会
  • Place of Presentation: つくば
  • Year and Date: 2015-06-17
• [Presentation] タンパク質複合体中の天然変性領域の振る舞い (2015)
  • Author(s): 七種和美、足立風水也、越阪部晃永、前澤拓也、西村善文、胡桃坂仁志、明石知子
  • Organizer: 第63回質量分析総合討論会、つくば（2015.6.17-19）
  • Place of Presentation: つくば
  • Year and Date: 2015-06-17
• [Presentation] テイル欠損したヌクレオソームの調製と修飾による構造変化の解析 (2014)
  • Author(s): 前澤拓也, 七種和美, 長土居有隆, 胡桃坂仁志, 西村善文, 明石知子
  • Organizer: 第87回日本生化学会大会
  • Place of Presentation: 京都
  • Year and Date: 2014-10-15 – 2014-10-18
• [Presentation] Behavior of the disordered tail regions of the histone H2A/H2B dimer (2014)
  • Author(s): Kazumi Saikusa, Aritaka Nagadoi, Kana Hara, Sotaro Fuchigami, Hitoshi Kurumizaka, Yoshifumi Nishimura and Satoko Akashi
  • Organizer: 20th International Conference on Mass Spectrometry
  • Place of Presentation: Geneva (Switzerland)
  • Year and Date: 2014-08-24 – 2014-08-28
• [Presentation] Native Mass Spectrometry of Reconstituted Human Nucleosome Core Particle (2014)
  • Author(s): Satoko Akashi, Nanako Azegami, Kazumi Saikusa, Yasuto Todokoro, Aritaka Nagadoi, Hitoshi Kurumizaka, Yoshifumi Nishimura
  • Organizer: 20th International Conference on Mass Spectrometry
  • Place of Presentation: Geneva (Switzerland)
  • Year and Date: 2014-08-24 – 2014-08-28
• [Presentation] Stability of the B2B3-beta crystallin heterodimer to increased oxidation by radical probe and ion mobility mass spectrometry (2014)
  • Author(s): Kevin Downard, Satoko Akashi, Simin Maleknia, Kazumi Saikusa
  • Organizer: 20th International Conference on Mass Spectrometry
  • Place of Presentation: Geneva (Switzerland)
  • Year and Date: 2014-08-24 – 2014-08-28
• [Presentation] ネイティブ質量分析 -タンパク質複合体のストイキオメトリーの確実な決定手法- (2014)
  • Author(s): 明石知子
  • Organizer: 第14回日本蛋白質科学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2014-06-25 – 2014-06-27