X-ray crystallography of RAGE (Receptor for Advanced Glycation Endproducts) involved in chronic diabetes

• Project/Area Number: 19770104
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Functional biochemistry
• Research Institution: The University of Tokyo (2008); Tokyo Institute of Technology (2007)
• Principal Investigator: ISHITANI Ryuichiro The University of Tokyo, 医科学研究所, 准教授 (30401186)
• Project Period (FY): 2007 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥3,810,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥510,000); Fiscal Year 2008: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2007: ¥1,600,000 (Direct Cost: ¥1,600,000)
• Keywords: 細胞情報伝達機構 / 糖尿病 / 血管障害 / 血管新生 / 後期糖化反応生成物 / アンフォテリン / S100A12蛋白質 / アミロイドβペプチド / X線結晶構造解 / X線結晶構造解析

Research Abstract

レセプター型RAGE のC末端細胞質ドメインと膜貫通ドメインを欠いた構造をもつスプライシングアイソフォーム、分泌型sRAGE(soluble RAGE)の結晶化スクリーニングを様々な条件について行った.また,低分子量の基質となりうる合成ペントシジンとの複合体の結晶化スクリーニングを行った.さらに,アンフォテリンとS100A12タンパク質を,sRAGEと同様に大腸菌における大量発現系を構築し,大量調製を行った.アンフォテリンに関しては,2通りの異なる領域を発現させるコンストラクトを作成し,それぞれ大量調製を行った.さらにsRAGEとの複合体の結晶化スクリーニングを行ったが,構造解析に適した結晶を得るには至らなかった.今後さらに,安定ドメインのみの発現系を作成し,大量調製,結晶化スクリーニングを行う予定である.

Research Products

• [Journal Article] Crystal structure of the cytosolic domain of the cation diffusion facilitator family protein (2009)
  • Author(s): Higuchi T, Hattori M, Tanaka Y, Ishitani R, and Nureki O
  • Journal Title: Proteins (in press)
  • Peer Reviewed
• [Journal Article] Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase (2009)
  • Author(s): Nishimasu H, Ishitani R, Yamashita K, Iwashita C, Hirata A, Hori H, and Nureki O
  • Journal Title: Proc. Natl Acad. Sci. U. S. A (in press)
  • Peer Reviewed
• [Journal Article] Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4 (2009)
  • Author(s): Suzuki Y, Noma A, Suzuki T, Ishitani R, and Nureki O
  • Journal Title: Nucleic Acids Res (in press)
  • Peer Reviewed
• [Journal Article] The structure of the pyrrolysyl-tRNA synthetase:tRNAPyl complex reveals the molecular basis of orthogonality (2009)
  • Author(s): Nozawa K, O'Donoghue P, Araiso Y, Gundllapalli S, Ishitani R, & Soll D, Nureki O
  • Journal Title: Nature 457 Pages: 1163-1167
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of GCIP/HHM transcriptional regulator (2009)
  • Author(s): Seto A, Ikushima H, Suzuki T, Sato Y, Fukai S, Yuki K, Miyazawa K, Miyazono K, Ishitani R, & Nureki O
  • Journal Title: Acta Crystallogr F65 Pages: 21-24
  • Peer Reviewed
• [Journal Article] Structural basis of tRNA modification with CO_2 fixation and methylation by wybutosine synthesizing enzyme TYW4 (2009)
  • Author(s): Suzuki Y, Noma A, Suzuki T, Ishitani R, Nureki O.
  • Journal Title: Nucleic Acids Res. (掲載確定)(未定)
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of GCIP/HHM transcriptional regulator (2009)
  • Author(s): Seto A, (他7名) Ishitani R and Nureki O
  • Journal Title: Acta Crystallogr Sect. F 65 Pages: 21-24
  • Peer Reviewed
• [Journal Article] The structure of the pyrrolysyl-tRNA synthetase : tRNAp^<Pyl> complex reveals the molecular basis of orthogonality (2009)
  • Author(s): Nozawa K, (他3名) Ishitani R, & Soli D, Nureki O.
  • Journal Title: Nature 457 Pages: 1163-1167
  • Peer Reviewed
• [Journal Article] The structure of the pyrrolysyl-tRNA synthetase : tRNA^<Pyl> complex reveals the molecular basis of orthogonality (2009)
  • Author(s): Nozawa K, (他3名) Ishitani R, & Soli D, Nureki O.
  • Journal Title: Nature 457 Pages: 1163-1167
  • Peer Reviewed
• [Journal Article] Structure, dynamics, and function of RNA modification enzyme (2009)
  • Author(s): Ishitani R, Yokoyama S, & Nureki O.
  • Journal Title: Curr. Opin. Struct. Biol 18 Pages: 330-339
  • Peer Reviewed
• [Journal Article] Conformational transition of Sec machinery inferred from bacterial SecYE structures (2008)
  • Author(s): Tsukazaki T, Mori H, Fukai S, Ishitani R, Mori T, Dohmae N, Perederina A, Sugita Y, Vassylyev D G, Ito K, & Nureki O
  • Journal Title: Nature 455 Pages: 988-991
  • Peer Reviewed
• [Journal Article] Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study (2008)
  • Author(s): Ishitani R, Sugita Y, Dohmae N, Furuya N, Hattori M, & Nureki O
  • Journal Title: Proc. Natl. Acad. Sci. U. S. A 105 Pages: 15393-15398
  • Peer Reviewed
• [Journal Article] Structure, dynamics, and function of RNA modification enzymes (2008)
  • Author(s): Ishitani R, Yokoyama S, & Nureki O
  • Journal Title: Curr. Opin. Struct. Biol 18 Pages: 330-339
  • Peer Reviewed
• [Journal Article] Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations (2008)
  • Author(s): Ishitani R, Terada T, & Shimizu K
  • Journal Title: Mol. Simul 34 Pages: 327-336
  • Peer Reviewed
• [Journal Article] Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation (2008)
  • Author(s): Araiso Y, Palioura S, Ishitani R, Sherrer R L, O'Donoghue P, Yuan J, Oshikane H, Domae N, Defranco J, Soll D, & Nureki O
  • Journal Title: Nucleic Acids Res 36 Pages: 1187-1199
  • Peer Reviewed
• [Journal Article] Conformational transition of Sec machinery inferred from bacterial SecYE structures (2008)
  • Author(s): Tsukazaki T, (他2名), Ishitani R, (他6名) & Nureki O.
  • Journal Title: Nature 455 Pages: 988-991
  • Peer Reviewed
• [Journal Article] Mg^<2+>-sensing mechanism of Mg^<2+> ansporter MgtE probed by mol ecular dynamics study (2008)
  • Author(s): Ishitani R, (他4名), & Nureki O.
  • Journal Title: Proc. Natl. Acad. Sci. U.S.A. 105 Pages: 15393-15398
  • Peer Reviewed
• [Journal Article] Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations (2008)
  • Author(s): Ishitani R, Terada T, & Shimizu K.
  • Journal Title: Mol. Simul. In press
  • Peer Reviewed
• [Journal Article] Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation (2008)
  • Author(s): Araiso Y, Palioura S, Ishitani R 他8名
  • Journal Title: Nucleic Acids Res. 36(4) Pages: 1187-1199
  • Peer Reviewed
• [Journal Article] Animated crystallography of genetic code translation (2007)
  • Author(s): Tomita K, Numata T, Fukai S, Ishitani R, & Nureki O
  • Journal Title: Nucleic Acids Symp. Ser 51 Pages: 101-102
  • Peer Reviewed
• [Journal Article] Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA (2007)
  • Author(s): Suzuki Y, Noma A, Suzuki T, Senda M, Senda T, Ishitani R, & Nureki O
  • Journal Title: J. Mol. Biol 372 Pages: 1204-1214
  • Peer Reviewed
• [Journal Article] Anticodon recognition and discrimination by the alpha-helix cage domain of class I lysyl-tRNA synthetase (2007)
  • Author(s): Levengood J D, Roy H, Ishitani R, Soll D, Nureki O, & Ibba M
  • Journal Title: Biochemistry 46 Pages: 11033-11038
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of the cytosolic domain of a cation diffusion facilitator family protein (2007)
  • Author(s): Hattori M, Tanaka Y, Ishitani R, & Nureki O
  • Journal Title: Acta Crystallogr F63 Pages: 771-773
  • Peer Reviewed
• [Journal Article] Crystal structure of the MgtE Mg2+ transporter (2007)
  • Author(s): Hattori M, Tanaka Y, Fukai S, Ishitani R, & Nureki O
  • Journal Title: Nature 448 Pages: 1072-1075
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of the full-length Mg2+ transporter MgtE (2007)
  • Author(s): Hattori M, Tanaka Y, Fukai S, Ishitani R, & Nureki O
  • Journal Title: Acta Crystallogr F63 Pages: 682-684
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of the cytosolic domain of the Mg2+ transporter MgtE (2007)
  • Author(s): Tanaka Y, Hattori M, Fukai S, Ishitania R, & Nureki O
  • Journal Title: Acta Crystallogr F63 Pages: 678-681
  • Peer Reviewed
• [Journal Article] Crystal structure of the Sec4p?Sec2p complex in the nucleotide exchanging intermediate state (2007)
  • Author(s): Sato Y, Fukai S, Ishitani R, & Nureki O
  • Journal Title: Proc. Natl Acad. Sci. U. S. A 104 Pages: 8305-8310
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of the cytosolic domain of a cation diffusion facilitator family protein (2007)
  • Author(s): Hattori M, Tanaka Y, Ishitani R, Nureki O
  • Journal Title: Acta Crystallogr. F63 Pages: 771-773
  • Peer Reviewed
• [Journal Article] Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA (2007)
  • Author(s): (5名) Ishitani R, Nureki O
  • Journal Title: J.Mbl. Biol. 372(5) Pages: 1204-1214
  • Peer Reviewed
• [Journal Article] Crystal structure of the MgtE Mg^2+ transporter (2007)
  • Author(s): Hattori M, Tanaka Y Fukai S, Ishitani R, Nureki O
  • Journal Title: Nature 448(7157) Pages: 1072-1075
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of the full-length Mg^2+ transporter MgtE (2007)
  • Author(s): Hattori M, Tanaka Y, Fukai S, Ishitani R, Nureki O
  • Journal Title: Acta Crystallogr. F63 Pages: 682-684
  • Peer Reviewed
• [Journal Article] Crystal structure of the Sec4p.Sec2p complex in the nucleotide exchanging intermediate state (2007)
  • Author(s): Sato Y, Fukai S, Ishitani R, Nureki O
  • Journal Title: Proc Natl Acad Sci U S A 104(20) Pages: 8305-8310
  • Peer Reviewed
• [Presentation] Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4 (2009)
  • Author(s): Suzuki Y, Noma A, Suzuki T, Ishitani R, and Nureki O
  • Organizer: Gordon Research Conference
  • Place of Presentation: アメリカ,ヒューストン
  • Year and Date: 2009-01-11
• [Presentation] Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study (2008)
  • Author(s): Ishitani R, Sugita Y, Dohmae N, Furuya N, Hattori M, & Nureki O
  • Organizer: Gordon Research Conference
  • Place of Presentation: イタリア,ルッカ
  • Year and Date: 2008-07-20
• [Presentation] マグネシウム輸送体MgtEの分子動力学シミュレーション (2008)
  • Author(s): 石谷隆一郎,杉田有治,濡木理
  • Organizer: 生物物理学会第46回年会
  • Place of Presentation: 福岡国際会議場
• [Presentation] マグネシウム輸送体MgtEの分子動力学シミュレーション (2007)
  • Author(s): 石谷隆一郎,杉田有治,濡木理
  • Organizer: 生物物理学会第45回年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2007-12-21
• [Presentation] Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA (2007)
  • Author(s): Ishitani R, Suzuki Y, Noma A, Suzuki T, Senda M, Senda T, & Nureki O
  • Organizer: tRNA workshop 2007
  • Place of Presentation: スウェーデン,ウプサラ
  • Year and Date: 2007-11-01