soft interaction for the recognition of mitochondrial targeting signal

• Project/Area Number: 15083205
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyushu University
• Principal Investigator: KOHDA Daisuke Kyushu University, 生体防御医学研究所, 教授 (80186618)
• Co-Investigator(Kenkyū-buntansha): MAENAKA Katsumi 九州大学, 生体防御医学研究所, 准教授 (10322752)
• Co-Investigator(Renkei-kenkyūsha): SAITOH Takashi 九州大学, デジタルメディシンイニシアティブ, 助教 (00432914)
• Project Period (FY): 2003 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥130,900,000 (Direct Cost: ¥130,900,000); Fiscal Year 2008: ¥16,000,000 (Direct Cost: ¥16,000,000); Fiscal Year 2007: ¥16,000,000 (Direct Cost: ¥16,000,000); Fiscal Year 2006: ¥14,400,000 (Direct Cost: ¥14,400,000); Fiscal Year 2005: ¥31,700,000 (Direct Cost: ¥31,700,000); Fiscal Year 2004: ¥16,000,000 (Direct Cost: ¥16,000,000); Fiscal Year 2003: ¥36,800,000 (Direct Cost: ¥36,800,000)
• Keywords: タンパク質 / ,分子認識 / 細胞内輸送 / ミトコンドリア / プレ配列 / 標的シグナル / Tom20 / リガンド係留技術 / 分子認識 / 分子内ジスルフィド結合 / 複合体安定化技術 / プレ配列受容体 / SS結合 / X線結晶解析 / NMR / 緩和時間解析 / X線結晶構造 / タンパク質輸送 / 構造生物学 / ペプチドライブラリ

Research Abstract

ミトコンドリア内部へ輸送されるタンパク質はN末端にプレ配列が付加されて生合成される.Tom20タンパク質はミトコンドリア外膜にあって,プレ配列を最初に認識する受容体である.Tom20とプレ配列の複合体を共有結合で安定化する技術を新規に考案して,結晶構造解析とNMR緩和時間解析を行った.複数の結合状態が存在するが,それぞれは認識としては不完全である.この複数の状態の間の速い動的平衡が,Tom20が多様なプレ配列を認識するメカニズムであることを提唱した.

Research Products

• [Journal Article] Structure-guided identification of a new catalytic motif of oligosaccharyltransferase (2008)
  • Author(s): Igura M, Maita N, Kamishikiryo J, Yamada M, Obita T, Maenaka K, Kohda D
  • Journal Title: EMBO J 27 Pages: 234-243
  • Peer Reviewed
• [Journal Article] ミトコンドリア行きシグナルを識別するためのソフトな分子認識 (2008)
  • Author(s): 神田大輔
  • Journal Title: 生化学 第80巻第10号 Pages: 888-896
  • NAID: 10022594528
• [Journal Article] Structure-guided identification of a new catalytic motif of oligosaccharyltransferase (2008)
  • Author(s): M. Igura, N. Maita, J. Kamishikiryo, M. Yamada, T. Obita, K. Maenaka, D. Kohda
  • Journal Title: EMBO J 27 Pages: 234-243
  • Peer Reviewed
• [Journal Article] Biophysical characterization of O-glycosylated CD99 recognition by paired Ig-like type 2 receptors (2008)
  • Author(s): S. Tabata, K. Kuroki, J. Wang, M. Kajikawa, I. Shiratori, D. Kohda, H. Arase, K. Maenaka
  • Journal Title: J Biol Chem 283 Pages: 8893-8893
  • Peer Reviewed
• [Journal Article] Complete Covalent Structure of Nisin Q, New Natural Nisin Variant, Containing Post-Translationally Modified Amino Acids (2008)
  • Author(s): M. Fukao, T. Obita, F. Yoneyama, D. Kohda, T. Zendo, J. Nakayama, K. Sonomoto
  • Journal Title: Biosci Biotechnol Biochem 72 Pages: 1750-1755
  • Peer Reviewed
• [Journal Article] Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA (2007)
  • Author(s): Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D
  • Journal Title: EMBO J 26 Pages: 2584-2593
  • Peer Reviewed
• [Journal Article] Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states (2007)
  • Author(s): Saitoh T, Igura M, Obita T, Ose T, Kojima R, Maenaka K, Endo T, Kohda D
  • Journal Title: EMBO J 26 Pages: 4777-4787
  • Peer Reviewed
• [Journal Article] New oligosaccharyltransferase assay method (2007)
  • Author(s): Kohda D, Yamada M, Igura M, Kamishikiryo J, Maenaka K
  • Journal Title: Glycobiology 17 Pages: 1175-1182
  • Peer Reviewed
• [Journal Article] Purification,crystallization and preliminary X-ray diffraction studies of the soluble domain of the oligosaccharyltransferase STT3 subunit from the thermophilic archaeon Pyrococcus furiosus (2007)
  • Author(s): Igura M, Maita N, Obita T, Kamishikiryo J, Maenaka K, Kohda D
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 63 Pages: 798-801
  • Peer Reviewed
• [Journal Article] Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA (2007)
  • Author(s): K., Sasaki, et. al.
  • Journal Title: EMBO Journal 26 Pages: 2584-2593
  • Peer Reviewed
• [Journal Article] New oligosaccharyltransferase assay method (2007)
  • Author(s): D., Kohda, et. al.
  • Journal Title: Glycobiology 17 Pages: 1175-1182
  • Peer Reviewed
• [Journal Article] Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states (2007)
  • Author(s): T., Saitoh, et. al.
  • Journal Title: EMBO Journal 26 Pages: 4777-4787
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli (2006)
  • Author(s): Sasaki K, Ose T, Tanaka T, Mizukoshi T, Ishigaki T, Maenaka K, Masai H, Kohda D
  • Journal Title: Biochim Biophys Acta 1764 Pages: 157-160
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherica is coli. (2006)
  • Author(s): K.Sasaki, T.Ose, T.Tanaka, T.Mizukoshi, T.Ishigaki, K.Maenaka, H.Masai, D.Kohda
  • Journal Title: Biochim. Biophys. Acta 1764 Pages: 157-160
• [Journal Article] Crystallization and preliminary X-ray analysis of mitochondrial presequence receptor Tom20 in complexes with a presequence from aldehyde dehydrogenase (2005)
  • Author(s): Igura M, Ose T, Obita T, Sato C, Maenaka K, Endo T, Kohda D
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun 61 Pages: 514-517
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray analysis of mitochondrial presequence receptor Tom20 in complexes with a presequence from aldehyde dehydrogenase (2005)
  • Author(s): M.Igura, T.Ose, T.Obita, C.Sato, K.Maenaka, T.Endo, D.Kohda
  • Journal Title: Acta Crystography F61 Pages: 514-517
• [Journal Article] Peptide library approach with a disulfide tether to refine the Tom20 recognition motif in mitochondrial presequences (2003)
  • Author(s): Obita, T, Muto, T, Endo, T, Kohda, D
  • Journal Title: J Mol Biol 328 Pages: 495-504
  • Peer Reviewed
• [Presentation] Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states (2009)
  • Author(s): Daisuke Kohda
  • Organizer: (invited, oral) 蛋白質立体構造解析NEDO 特別講座 国際シンポジウム2009
  • Place of Presentation: 東京
  • Year and Date: 2009-01-26
• [Presentation] Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states (2009)
  • Author(s): Daisuke Kohda
  • Organizer: 蛋白質立体構造解析NEDO特別講座国際シンポジウム2009
  • Place of Presentation: 東京
  • Year and Date: 2009-01-26
• [Presentation] Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states - Complex stabilization with a molecular tether - (invited,oral) (2009)
  • Author(s): Daisuke Kohda
  • Organizer: International Symposium on Molecular Soft Interactions in Biological Systems Organized by The Priority Area ゛Membrane Interface゛
  • Place of Presentation: Osaka
• [Presentation] Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states (2009)
  • Author(s): Daisuke Kohda
  • Organizer: International Symposium on Molecular Soft Interactions in Biological Systems
  • Place of Presentation: Osaka
• [Presentation] 「複数の結合様式を介したミトコンドリアTom20によるプレ配列の認識機構」(口頭発,若手奨励賞シンポジウム) (2008)
  • Author(s): 斉藤貴士
  • Organizer: 第8回日本蛋白質科学会年会
  • Place of Presentation: 東京
  • Year and Date: 2008-06-11
• [Presentation] Relaxation analysis of the Tom20-bound states of a mitochondrial presequence (2008)
  • Author(s): Takashi Saitoh
  • Organizer: International Conference on Magnetic Resonance in Biological Systems (XXIII ICMRBS)
  • Place of Presentation: San Diego, USA
• [Presentation] Structure-guided identification of a new catalytic motif of oligosaccharyltransferase (2008)
  • Author(s): Daisuke Kohda
  • Organizer: Fukuoka Symposium on Molecular Soft Interactions at Biomembrane Interface
  • Place of Presentation: Fukuoka
• [Presentation] 「アスパラギン結合型糖鎖修飾を決定するオリゴ糖転移酵素の構造生化学」(シンポジウム口演) (2007)
  • Author(s): 神田大輔
  • Organizer: 第27回日本糖質学会年会
  • Place of Presentation: 福岡
  • Year and Date: 2007-08-02
• [Presentation] ミトコンドリアTom20によるプレ配列の動的認識機構:緩和解析からのアプローチ(ワークショップにおける口頭発表) (2007)
  • Author(s): 齋藤 貴士
  • Organizer: 第7回日本蛋白質科学会年会
  • Place of Presentation: 仙台国際センター
  • Year and Date: 2007-05-26
• [Presentation] Asn結合型糖鎖修飾を決定するオリゴ糖転移酵素の構造生物学研究(ワークショップ口演) (2007)
  • Author(s): 井倉真由美
  • Organizer: 第7回日本蛋白質科学会年会
  • Place of Presentation: 仙台
• [Presentation] ミトコンドリアTom20によるプレ配列の動的認識機構:緩和解析からのアプローチ(ワークショップ口演) (2007)
  • Author(s): 齊藤貴士
  • Organizer: 第7回日本蛋白質科学会年会
  • Place of Presentation: 仙台
• [Presentation] Relaxation study reveals a dual-mode interaction mechanism for mitochondrial presequence recognition by Tom20 (2007)
  • Author(s): Daisuke Kohda
  • Organizer: (invited, oral)International Workshop on Perspectives on stable isotope aided NMR methods for protein structural analysis
  • Place of Presentation: Osaka
• [Presentation] Recognize not to discriminate : mechanism of nonselective base recognition of 3'-terminus of DNA by PriA protein (2006)
  • Author(s): Daisuke Kohda
  • Organizer: (invited, oral)The 2nd Sapporo Conference 2006 ; New Trend in Structural Biology
  • Place of Presentation: Sapporo
• [Presentation] Dynamic recognition of mitochondrial presequences by Tom20 (2006)
  • Author(s): Takashi Saitoh
  • Organizer: The 2nd Sapporo Conference 2006; New Trend in Structural Biology
  • Place of Presentation: Sapporo
• [Presentation] Tom20 receptor recognizes the mitochondrial presequence through dynamic equilibrium (2006)
  • Author(s): Mayumi Igura
  • Organizer: 20th IUBMB International Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress
  • Place of Presentation: Kyoto
• [Presentation] 「ゆるい相互作用をX線結晶解析とNMRで見る」(ワークショップ口演) (2006)
  • Author(s): 神田大輔
  • Organizer: 第6回日本蛋白質科学会
  • Place of Presentation: 京都
• [Presentation] <ゆるい>相互作用に対する構造生物学アプローチ (2005)
  • Author(s): 神田大輔
  • Organizer: よこはまNMR構造生物学研究会第27回ワークショップ「細胞シグナリングの構造生物学」
  • Place of Presentation: 横浜
  • Year and Date: 2005-09-21
• [Presentation] Crystal structures conformationally locked with a disulfide tether suggest a dual-mode interaction mechanism for mitochondrial presequence recognition by Tom20 (2005)
  • Author(s): Takayuki Obita
  • Organizer: International Symposium on Life of Proteins
  • Place of Presentation: Hyogo
• [Presentation] Cracking of the targeting signal embedded in mitochondrial presequences (2005)
  • Author(s): Daisuke Kohda
  • Organizer: (invited, oral)XX Congress of the International Union of Crystallography Florence
  • Place of Presentation: Italy
• [Presentation] Cracking of the targeting signal embedded in mitochondrial presequences (2005)
  • Author(s): Mayumi Igura
  • Organizer: XX Congress of the International Union of Crystallography Florence
  • Place of Presentation: Italy
• [Presentation] ミトコンドリアへの標的シグナルを構造の観点から解読する (2004)
  • Author(s): 神田大輔
  • Organizer: 第26回生体膜と薬物の相互作用シンポジウム
  • Place of Presentation: 東京
  • Year and Date: 2004-11-25
• [Presentation] ミトコンドリアへの標的シグナルを構造の観点から解読する (2004)
  • Author(s): 神田大輔
  • Organizer: 2004蛋白研セミナー「生体系NMRにおける技術革新」
  • Place of Presentation: 大阪
  • Year and Date: 2004-11-19
• [Presentation] Disulfide bond tethering approach for the study of molecular interactions (2004)
  • Author(s): Daisuke Kohda
  • Organizer: 特定領域研究「膜インタフェイス」第2回公開シンポジウムMolecular Soft Interactions at Biomembrane Interface
  • Place of Presentation: 大阪
  • Year and Date: 2004-08-04
• [Presentation] "Structural basis of the decoding of the mitochondrial targeting signals by Tom20 (2004)
  • Author(s): Takayuki Obita
  • Organizer: The 1st Pacific-Rim International Conference on Protein Science
  • Place of Presentation: Yokohama
• [Presentation] Cracking of the targeting signal embedded in mitochondrial presequences by NMR and crystallography (2004)
  • Author(s): Daisuke Kohda
  • Organizer: (invited, oral)UK-Japan Structural Genomics Conference UK/Japan Symposium
  • Place of Presentation: Oxford UK
• [Presentation] Cracking of the targeting signal embedded in mitochondrial presequences by NMR and crystallography (2004)
  • Author(s): Daisuke Kohda
  • Organizer: (invited, oral)CREST internationalsymposium, Frontier of Biological NMR Spectroscopy
  • Place of Presentation: OSAKA
• [Remarks]
  • URL: http://www.bioreg.kyushu-u.ac.jp/vsb/index.html
• [Publications] Obita, T.et al.: "Peptide library approach with a disulfide tether to refine the Tom20 recognition motif in mitochondrial presequences"Journal of molecular biology. 328. 495-504 (2003)