Structural analysis to investigate the coordinating role of DNA clamp in replisome

• Project/Area Number: 24370046
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Kyushu University
• Principal Investigator: Mayanagi Kouta 九州大学, 生体防御医学研究所, 助教 (50418571)
• Co-Investigator(Kenkyū-buntansha): SHIRAI Tsuyoshi 長浜バイオ大学, 教授 (00262890) ; OYAMA Takuji 山梨大学, 准教授 (60423133)
• Co-Investigator(Renkei-kenkyūsha): ISHINO Yoshizumi 九州大学, (連合)農学研究科, 教授 (30346837)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000); Fiscal Year 2015: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000); Fiscal Year 2014: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2013: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2012: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
• Keywords: 電子顕微鏡 / ナノバイオ / 生体分子 / 可視化 / 生物物理 / 画像解析 / 複合体 / 立体構造 / 単粒子解析 / DNA複製 / クランプ

Outline of Final Research Achievements

PCNA has a trimeric ring structure that encircles the DNA, and increases the processivity of the bound DNA polymerase by tethering it to the DNA. It is known now, that PCNA also interacts with multiple partners, such as DNA ligase and FEN, to control DNA replication, and works not only as the platform, but also as the conductor for the recruitment and release of these factors. However, the molecular architectures as well as the mechanism of the regulation of these replication factors are not known in detail. In order to investigate the switching mechanism between the replication factors in more detail, we studied the complex structures with two replication factors bound to one PCNA ring, by single particle analysis. We could successfully visualize the 3D structure of FEN-DNA ligase-PCNA-DNA complex, the intermediate state of Okazaki fragment maturation, and the handing over of the ds DNA strand from FEN to DNA ligase.

Research Products

• [Journal Article] Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea. (2016)
  • Author(s): Ishino S, Nishi Y, Oda S, Uemori T, Sagara T, Takatsu N, Yamagami T, Shirai T, Ishino Y.
  • Journal Title: Nucleic Acid Res. Volume: 124 Pages: 2977-2086
  • DOI: 10.1093/nar/gkw153
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Novel AVPR2 mutation causing partial nephrogenic diabetes insipidus in a Japanese family (2016)
  • Author(s): Yamashita S, Hata A, Usui T, Oda H, Hijikata A, Shirai T, Kaneko N, Hata D
  • Journal Title: J Pediatr Endocrinol Metab Volume: 5 Pages: 591-596
  • DOI: 10.1515/jpem-2015-0323
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Integrated molecular mechanism directing nucleosome reorganization by human FACT (2016)
  • Author(s): Tsunaka Y, Fujiwara Y, Oyama T, Hirose S, Morikawa K
  • Journal Title: Gense & Development Volume: 30(6) Pages: 673-686
  • DOI: 10.1101/gad.274183.115
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling (2015)
  • Author(s): Toshiyuki Tsuji, Takao Yoda, and Tsuyoshi Shirai
  • Journal Title: Scientific Reports Volume: 5 Pages: 16341-16341
  • DOI: 10.1038/srep16341
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The influence of PRNP polymorphisms on human prion disease susceptibility: an update (2015)
  • Author(s): Kobayashi A, Teruya K, Matsuura Y, Shirai T, Nakamura Y, Yamada M, Mizusawa H, Mohri S, Kitamoto T.
  • Journal Title: Acta Neuropathol. Volume: 130 Pages: 159-170
  • DOI: 10.1007/s00401-015-1447-7
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] 超分子モデリングによる創薬支援 (2015)
  • Author(s): 土方敦司、辻 敏之、白井 剛
  • Journal Title: SAR News Volume: 28 Pages: 1-7
• [Journal Article] Peroxisome proliferator-activated receptor gamma (PPARgamma) has multiple binding points that accommodate ligands in various conformations: Structurally similar PPARgamma partial agonists bind to PPARgamma LBD in different conformations (2015)
  • Author(s): Ohashi M, Gamo K, Oyama T, Miyachi H
  • Journal Title: Bioorg. Med. Chem. Lett Volume: 25 Pages: 2758-2762
  • DOI: 10.1016/j.bmcl.2015.05.025
  • Peer Reviewed
• [Journal Article] Different structures of the two peroxisome proliferator-activated receptor gamma (PPARγ) ligand-binding domains in homodimeric complex with partial agonist, but not full agonist (2015)
  • Author(s): M. Ohashi, T. Oyama, H. Miyachi
  • Journal Title: Bioorg. Med. Chem. Lett. Volume: - Pages: 2639-2644
  • DOI: 10.1016/j.bmcl.2015.04.076
  • Peer Reviewed
• [Journal Article] Structural design and synthesis of arylalkynyl amide-type peroxisome proliferator-activated receptor γ (PPARγ)-selective antagonists based on the helix12-folding inhibition hypothesis. (2015)
  • Author(s): M. Ohashi, K. Gamo, Y. Tanaka, M. Waki, Y. Beniyama, K. Matsuno, J. Wada, M. Tenta, J. Eguchi, M. Makishima, N. Matsuura, T. Oyama, H. Miyachi.
  • Journal Title: Eur J Med Chem Volume: 90 Pages: 53-67
  • DOI: 10.1016/j.ejmech.2014.11.017
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Disordered interdomain region of Gins is important for functional tetramer formation to stimulate MCM helicase in Thermoplasma acidophilum (2015)
  • Author(s): Ogino H, Ishino S, Oyama T, Kohda D, Ishino Y
  • Journal Title: Bioscience, Biotechnology, and Biochemistry Volume: 79 Pages: 432-438
  • DOI: 10.1080/09168451.2014.982503
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Revealing the intracellular ultrastructure of filopodia with cryo-electron tomography. (2014)
  • Author(s): Shinji Aramaki, Kouta Mayanagi, Kazuhiro Aoyama and Takuo Yasunaga
  • Journal Title: Microscopy Volume: 63 Pages: 133-134
  • DOI: 10.1093/jmicro/dfu071
  • Peer Reviewed
• [Journal Article] 単粒子解析法で迫るDNA 複製フォーク複合体の機能構造連関 (2014)
  • Author(s): 真柳浩太
  • Journal Title: 顕微鏡 Volume: 49 Pages: 110-117
  • NAID: 130007701713
  • Peer Reviewed
• [Journal Article] Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities (2014)
  • Author(s): Ohtana Y,Abdullah AA, Amin MA,Huang M,Ono N, Sato T,Sugiura T,Horai H,Nakamura Y,Morita AH, Lange KW,Kibinge NK, Katsuragi T,Shirai T,Kanaya S
  • Journal Title: Mol. Inform. Volume: 33 Pages: 790-801
  • DOI: 10.1002/minf.201400123
  • NAID: 130005146305
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Aicardi-Goutières syndrome is caused by IFIH1 mutations. (2014)
  • Author(s): Oda, H., Nakagawa, K., Abe, J., Awaya, T., Funabiki, M., Hijikata, A., Nishikomori, R., Funatsuka, M., Ohshima, Y., Sugawara, Y., Yasumi, T., Kato, H., Shirai, T., Ohara, O., Fujita, T., Heike, T.
  • Journal Title: Am. J. Hum. Genet. Volume: 95 Pages: 121-125
  • DOI: 10.1016/j.ajhg.2014.06.007
  • NAID: 120005460706
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Evaluating Prion Models Based on Comprehensive Mutation Data of Mouse PrP. (2014)
  • Author(s): Shirai T, Saito M, Kobayashi A, Asano M, Hizume M, Ikeda S, Teruya K, Morita M, Kitamoto T.
  • Journal Title: Structure Volume: 22 Pages: 560-571
  • DOI: 10.1016/j.str.2013.12.019
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of domain chimeric L-(2S, 3S)-butanediol dehydrogenase (2014)
  • Author(s): Shimegi T, Oyama T, Ohtsuki T, Kurisu G, Kusunoki M, Ui S
  • Journal Title: Acta Cryst F Volume: 70 Pages: 461-463
  • DOI: 10.1107/s2053230x13032755
  • Peer Reviewed
• [Journal Article] Purification and characterization of a protease from Isaria cicadae (2014)
  • Author(s): Takekawa C, Nakamura K, Homma H, Oyama T
  • Journal Title: Mushroom Science and Biotechnology Volume: 22 Pages: 74-78
  • NAID: 110009863113
  • Peer Reviewed
• [Journal Article] Molecular dynamics study-guided identification of cyclic amine structures as novel hydrophobic tail components of hPPARγ agonists (2014)
  • Author(s): Tanaka Y, Gamo K, Oyama T, Ohashi M, Waki M, Matsuo K, Matsuura N, Tokiwa H, Miyachi H
  • Journal Title: Bioorg Med Chem Volume: 24 Pages: 4001-4005
  • DOI: 10.1016/j.bmcl.2015.06.023
  • Peer Reviewed
• [Journal Article] Structure of the entire stalk region of the dynein motor domain (2014)
  • Author(s): Yosuke Nishikawa, Takuji Oyama, Narutoshi Kamiya, Takahide Kon, Yoko Y. Toyoshima, Haruki Nakamura, Genji Kurisu
  • Journal Title: J. Mol. Biol. Volume: 426 Pages: 3232-3245
  • DOI: 10.1016/j.jmb.2014.06.023
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Modification of Chimeric (2S, 3S)-butanediol dehydrogenase based on structural information (2014)
  • Author(s): Shimegi T, Mochizuki K, Oyama T, Kusunoki M, Ui S
  • Journal Title: Protein Pept Lett Volume: 22 Pages: 226-233
  • Peer Reviewed
• [Journal Article] The centromeric nucleosome-like CENP-T-W-S-X complex induces positive supercoils into DNA. (2014)
  • Author(s): Kozo Takeuchi, Tatsuya Nishino, Kouta Mayanagi, Naoki Horikoshi, Akihisa Osakabe, Hiroaki Tachiwana, Tetsuya Hori, Hitoshi Kurumizaka and Tatsuo Fukagawa.
  • Journal Title: Nucleic Acid Research Volume: 42 Pages: 16441655-16441655
  • DOI: 10.1093/nar/gkt1124
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] データベース解析によるタンパク質リガンドの多様性 (2013)
  • Author(s): 白井 剛
  • Journal Title: 生化学 Volume: 85 Pages: 671-687
  • NAID: 10031195378
• [Journal Article] Structure of novel enzyme in mannan biodegradation process 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP (2013)
  • Author(s): Setsu Nakae, Shigeaki Ito, Mariko Higa, Takeshi Senoura, Jun Wasaki, Atsushi Hijikata, Masafumi Shionyu, Susumu Ito, Tsuyoshi Shirai
  • Journal Title: J. Mol. Biol. Volume: 425 Pages: 4468-4478
  • DOI: 10.1016/j.jmb.2013.08.002
  • Peer Reviewed
• [Journal Article] X-ray structure analysis and characterization of AFUEI, an elastase inhibitor from Aspergillus fumigatus (2013)
  • Author(s): Mayuko Sakuma, Katsumi Imada, Yoshiyuki Okumura, Kei-ichi Uchiya, Nobuo Yamashita, Kenji Ogawa, Atsushi Hijikata, Tsuyoshi Shirai, Michio Homma, Toshiaki Nikai
  • Journal Title: J. Biol. Chem. Volume: 288 Pages: 17451-17459
  • DOI: 10.1074/jbc.m112.433987
  • Peer Reviewed
• [Journal Article] Mutational and Structural Analyses of Caldanaerobius polysaccharolyticus Man5B Reveal Novel Active Site Residues for Family 5 Glycoside Hydrolases (2013)
  • Author(s): Takuji Oyama, George E Schmitz, Dylan Dodd, Yejun Han, Alanna Burnett, Naoko Nagasawa, Roderick I Mackie, Haruki Nakamura, Kosuke Morikawa, & Isaac Cann
  • Journal Title: PLoS One Volume: 8
  • DOI: 10.1371/journal.pone.0080448
  • Peer Reviewed
• [Journal Article] Crystal Structures Of Copper-Depleted And Copper-Bound Fungal Pro-Tyrosinase: Insights Into Endogenous Cysteine-Dependent Copper Incorporation (2013)
  • Author(s): Shinobu Itoh, et al.
  • Journal Title: J. Biol. Chem. Volume: 288 Pages: 22128-22
  • DOI: 10.1074/jbc.m113.477612
  • Peer Reviewed
• [Journal Article] Design and synthesis of a series of a-benzyl phenylpropanoic acid-type peroxisome proliferator-activated receptor (PPAR) gamma partial agonists with improved a queous solubility. (2013)
  • Author(s): Ohashi, M., Oyama, T., Putranto, E. W., Waku, T., Nobusada, H., Kataoka, K., Matsuno, K., Yashiro, M., Morikawa, K., Huh, N. H., Miyachi, H.
  • Journal Title: Bioorg Med Chem Volume: 21 Issue: 8 Pages: 2319-2332
  • DOI: 10.1016/j.bmc.2013.02.003
  • Description: in press
  • Peer Reviewed
• [Journal Article] Classification of Iigand molecules in PDB with fast heuristics graph match algorithm COMPLIG (2012)
  • Author(s): Saito M, Takemura N, Shirai T
  • Journal Title: J. Mol. Biol. Volume: 424 Pages: 379-390
  • DOI: 10.1016/j.jmb.2012.10.001
  • Peer Reviewed
• [Journal Article] Supramolecule Modeling: The Mechanism of Switching between Polymerization – Proof Reading Modes in DNA Duplication (2012)
  • Author(s): 白井 剛
  • Journal Title: Biophysics Volume: 52 Issue: 5 Pages: 246-249
  • DOI: 10.2142/biophys.52.246
  • NAID: 10030877059
  • ISSN: 0582-4052, 1347-4219
  • Peer Reviewed
• [Journal Article] 祖先遺伝子推定による古代タンパク質の解析 (2012)
  • Author(s): 白井 剛
  • Journal Title: 生物工学 Volume: 12 Pages: 11-14
  • NAID: 110009580295
  • Peer Reviewed
• [Journal Article] Bidirectional fluorescence properties of pyrene-based peroxisome proliferator-activated receptor (PPAR) α/δ dual agonist. (2012)
  • Author(s): Ban, S., Oyama, T., Kasuga, J. I., Ohgane, K., Nishio, Y., Morikawa, K., Hashimoto, Y. & Miyachi, H.
  • Journal Title: Bioorg Med Chem Volume: 20 Issue: 11 Pages: 3460-3464
  • DOI: 10.1016/j.bmc.2012.04.015
  • Peer Reviewed
• [Presentation] 超好熱性アーキアThermococcus kodakarensis由来ファミリーD DNAホリメラーセの構造と機能の相関 (2015)
  • Author(s): 高島 夏希, 石野 園子，高藤 三加，真柳 浩太，原 智彦，山上 健，石野 良純
  • Organizer: 第38回日本分子生物学会年会・第88回日本生化学会大会・合同大会
  • Place of Presentation: 兵庫県神戸市
  • Year and Date: 2015-12-01
• [Presentation] Single particle analysis of DNA replication fork complex (2015)
  • Author(s): Kouta Mayanagi
  • Organizer: The 25th Hot Spring Harbor International Symposium
  • Place of Presentation: Fukuoka, Japan
  • Year and Date: 2015-11-13
  • Int'l Joint Research
• [Presentation] DNA複製フォーク複合体の構築原理及び遷移•制御機構の解明 (2015)
  • Author(s): 真柳浩太
  • Organizer: さきがけ-ライフサイエンスの革新を目指した構造生命科学と先端的基盤技術- 研究領域 研究成果報告会
  • Place of Presentation: 東京都文京区
  • Year and Date: 2015-11-09
• [Presentation] Development of a protein-protein docking method based on matching of vector-presented amino acid residues (2015)
  • Author(s): Hijikata A, Shionyu M, Shirai T
  • Organizer: 生命医薬情報学連合大会2015年大会
  • Place of Presentation: 京都府宇治市
  • Year and Date: 2015-10-29
• [Presentation] タンパク質超分子モデリングによる疾患関連変異の解析 (2015)
  • Author(s): 辻 敏之, 依田隆夫, 白井 剛
  • Organizer: 生命医薬情報学連合大会2015年大会
  • Place of Presentation: 京都府宇治市
  • Year and Date: 2015-10-29
• [Presentation] Analyzing disease-related amino acid variants with protein supramolecule modeling (2015)
  • Author(s): 辻 敏之, 依田隆夫, 白井 剛
  • Organizer: 生命医薬情報学連合大会2015年大会
  • Place of Presentation: 京都府宇治市
  • Year and Date: 2015-10-29
• [Presentation] 擬似リン酸化によるMEK1の構造変化 (2015)
  • Author(s): 中江 摂, 白井 剛, 桐井康行, 多田俊治
  • Organizer: 平成27年度日本結晶学会年会
  • Place of Presentation: 大阪府堺市
  • Year and Date: 2015-10-17
• [Presentation] A statistical amino acid pair potential to re-rank protein-protein docking poses predicted by a vector match algorithm (2015)
  • Author(s): Hijikata A, Shionyu M, Shirai T
  • Organizer: 第53回日本生物物理学会年会
  • Place of Presentation: 石川県金沢市
  • Year and Date: 2015-09-13
• [Presentation] Structure prediction and analyses of endonuclease NucS from Thermococcus kodakaraensis (2015)
  • Author(s): Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama K, Mayanagi K, Ishino S, Ishino Y, Shirai T
  • Organizer: 第53回日本生物物理学会年会
  • Place of Presentation: 石川県金沢市
  • Year and Date: 2015-09-13
• [Presentation] Relationship between protein-protein interaction interface predicted by complex modeling and disease-related amino acid variants (2015)
  • Author(s): 辻 敏之, 依田隆夫, 白井 剛
  • Organizer: 第53回日本生物物理学会年会
  • Place of Presentation: 石川県金沢市
  • Year and Date: 2015-09-13
• [Presentation] A method for scoring protein docking-poses on the basis of protein-protein interactions statistics (2015)
  • Author(s): Hijikata A, Shionyu M, Shirai T,
  • Organizer: 第15回日本蛋白質科学会年会
  • Place of Presentation: 徳島県徳島市
  • Year and Date: 2015-06-24
• [Presentation] マルチドメインタンパク質の構造予測サーバの構築 (2015)
  • Author(s): 塩生真史, 土方敦司, 白井 剛
  • Organizer: 第15回日本蛋白質科学会年会
  • Place of Presentation: 徳島県徳島市
  • Year and Date: 2015-06-24
• [Presentation] Development of method for protein-protein interaction modeling using IntAct database (2015)
  • Author(s): 辻 敏之, 依田隆夫, 白井 剛
  • Organizer: 第15回日本蛋白質科学会年会
  • Place of Presentation: 徳島県徳島市
  • Year and Date: 2015-06-24
• [Presentation] タンパク質相互作用データベースを利用した超分子モデリング法の開発 (2015)
  • Author(s): 辻 敏之, 依田隆夫, 白井 剛
  • Organizer: 第15回日本蛋白質科学会年会
  • Place of Presentation: 徳島県徳島市
  • Year and Date: 2015-06-24
• [Presentation] Architecture and Regulation Mechanism of DNA Replication Fork Complex Revealed by Single Particle Analysis (2015)
  • Author(s): Mayanagi K
  • Organizer: IGER International Symposium on Frontiers in Biological Research with Advanced Electron Microscope Technologies
  • Place of Presentation: 名古屋大学、名古屋
  • Year and Date: 2015-01-15 – 2015-01-16
  • Invited
• [Presentation] Revealing the intracellular ultrastructure of filopodia with cryo-electron tomography (2014)
  • Author(s): Aramaki S, Mayanagi K, Aoyama K, Yasunaga T
  • Organizer: 日本顕微鏡学会第５８回シンポジウム
  • Place of Presentation: 九州大学、福岡
  • Year and Date: 2014-11-16 – 2014-11-17
• [Presentation] 単粒子解析によるDNA複製フォーク複合体の機能構造連関の研究 (2014)
  • Author(s): 真柳浩太
  • Organizer: 京都大学放射線生物研究センターセミナー
  • Place of Presentation: 京都大学、京都
  • Year and Date: 2014-11-07
  • Invited
• [Presentation] 大豆イソフラボングルコシルトランスフェラーゼGmIF7GTの結晶構造解析 (2014)
  • Author(s): 桑名美貴子、楠木正巳、大山拓次、中山亨
  • Organizer: 平成26年度日本結晶学会年会
  • Place of Presentation: 東京大学、東京
  • Year and Date: 2014-11-01 – 2014-11-03
• [Presentation] 大豆イソフラボングルコシルトランスフェラーゼGmIF7GTの構造生物学 (2014)
  • Author(s): 桑名美貴子、楠木正巳、大山拓次、中山亨
  • Organizer: 第87回日本生化学会年会
  • Place of Presentation: 国立京都国際会館、京都
  • Year and Date: 2014-10-15 – 2014-10-18
• [Presentation] Supramolecular modeling pipeline for correlative structural analysis and rational drug-design (2014)
  • Author(s): 白井 剛
  • Organizer: 第５２回日本生物物理学会年会
  • Place of Presentation: 札幌コンベンションセンター、札幌
  • Year and Date: 2014-09-25 – 2014-09-27
  • Invited
• [Presentation] イントロダクション:3D遺伝学のすすめ (2014)
  • Author(s): 白井 剛
  • Organizer: 第86回遺伝学会年会
  • Place of Presentation: 長浜バイオ大学、滋賀
  • Year and Date: 2014-09-17 – 2014-09-19
• [Presentation] Single particle analysis of molecular architecture of DNA replication fork complex and switching mechanism of replication factors (2014)
  • Author(s): Mayanagi K, Kiyonari S, Nishida H, Ishino S, Fujikane R, Saito M, Kohda D, Ishino Y, Shirai T, Morikawa K, Mayanagi K, Kiyonari S, Nishida H, Ishino S, Saito M, Kohda D, Ishino Y, Shirai T, Morikawa
  • Organizer: 18th International Microscopy Congress
  • Place of Presentation: Prague Czech, Republic
  • Year and Date: 2014-09-07 – 2014-09-12
• [Presentation] 超分子モデリングパイプラインの構築による相関構造解析・理論創薬支援 (2014)
  • Author(s): 白井 剛
  • Organizer: 第14回日本蛋白質科学会年会
  • Place of Presentation: ワークピア横浜、横浜
  • Year and Date: 2014-06-25 – 2014-06-27
  • Invited
• [Presentation] 超分子モデリングパイプラインの構築 (2014)
  • Author(s): 白井 剛
  • Organizer: 創薬等支援技術基盤プラットフォームテクニカルセミナー2014
  • Place of Presentation: 名古屋大学、名古屋
  • Year and Date: 2014-06-24
  • Invited
• [Presentation] Molecular architecture and switching mechanism of the replication fork complex (2014)
  • Author(s): Mayanagi K, Kiyonari S, Nishida H, Ishino S, Saito M, Kohda D, Ishino Y, Shirai T, Morikawa K
  • Organizer: Gordon Research Conference,Three Dimensional Electron Microscopy
  • Place of Presentation: Girona, Spain
  • Year and Date: 2014-06-22 – 2014-06-27
• [Presentation] DNA複製フォーク複合体の分子構築及び切換え機構の研究 (2014)
  • Author(s): 真柳浩太
  • Organizer: タンパク質研究所セミナー
  • Place of Presentation: 大阪
  • Invited
• [Presentation] Molecular architecture and switching mechanism of DNA replication fork complex (2013)
  • Author(s): Kouta Mayanagi
  • Organizer: Gordon Research Conference,Three Dimensional Electron Microscopy
  • Place of Presentation: Colby-Sawyer College, NH, USA
• [Presentation] Electron microscopic analysis of molecular architecture and switching mechanism of DNA replication fork complex (2013)
  • Author(s): Kouta Mayanagi, Shinichi Kiyonari, Hirokazu Nishida, Sonoko Ishino, Mihoko Saito, Daisuke Kohda, Yoshizumi Ishino, Tsuyoshi Shirai, Kosuke Morikawa
  • Organizer: ICSG2013-SLS
  • Place of Presentation: 札幌
• [Presentation] Electron microscopic structure analysis of protein-DNA complexes (2013)
  • Author(s): Kouta Mayanagi
  • Organizer: The 3rd International conference on New Frontier of the Research on RecA-family recombinases and their accessory proteins
  • Place of Presentation: Nantes, France
• [Presentation] Activation mechanism of the replicative helicase in the thermophilic archaeon, Thermoplasma acidophilum (2013)
  • Author(s): Hiromi Ogino, Sonoko Ishino, Kouta Mayanagi, Takuji Oyama, Tsuyoshi Shirai, Kosuke Morikawa, Gyri Teien Haugland, Nils-Kare Birkeland, Daisuke Kohda, Yoshizumi Ishino
  • Organizer: Thermophiles 2013
  • Place of Presentation: Regensburg, Germany
• [Presentation] 組み替えhuman poly(ADP-ribose) polymerase 1の精製と予備的構造解析 (2013)
  • Author(s): Kenichi Koyama, Kouta Mayanagi, Takayuki Eguchi, Hiroyuki Morita, Kazuo Kamemura, Yoshisuke Nishi, Masanao Miwa Tsuyoshi Shirai
  • Organizer: 第８６回日本生化学会大会
  • Place of Presentation: 横浜
• [Presentation] 好熱性アーキアThermoplasma acidophilumにおける複製ヘリカーゼ活性化機構の分岐進化 (2013)
  • Author(s): 尾木野 弘実, 石野 園子, 真柳 浩太, 大山 拓次, 白井 剛, 森川 耿右, Haugland Gyri Teien, Birkeland Nils-Kare, 神田 大輔, 石野 良純
  • Organizer: 第１４回極限環境生物学会
  • Place of Presentation: 川崎
• [Presentation] DNA 複製に関与する超分子複合体の単粒子解析 (2013)
  • Author(s): 真柳浩太
  • Organizer: 日本顕微鏡学会第57回シンポジウム
  • Place of Presentation: 名古屋
  • Invited
• [Presentation] Divergently evolved activation mechanism of the replicative helicase in the thermophilic archaeon, Thermoplasma acidophilum (2013)
  • Author(s): Hiromi Ogino, Sonoko Ishino, Kouta Mayanagi, Takuji Oyama, Tsuyoshi Shirai, Kosuke Morikawa, Gyri Teien Haugland, Nils-Kare Birkeland, Daisuke Kohda, Yoshizumi Ishino
  • Organizer: 第36回日本分子生物学会
  • Place of Presentation: 神戸
• [Presentation] 組み替えhuman poly(ADP-ribose) polymerase 1の精製とその立体構造解析 (2013)
  • Author(s): Kenichi Koyama, Takayuki Eguchi, Hiroyuki Morita, Kazuo Kamemura, Yoshisuke Nishi, Masanao Miwa Tsuyoshi Shirai
  • Organizer: 生物物理学会年会
  • Place of Presentation: 京都
• [Presentation] 4-O-β-D-mannosyl-D-glucose phosphorylase (MGP) のＸ線結晶構造解析 (2013)
  • Author(s): Setsu Nakae,Shigeaki Ito, Mariko Higa, Takeshi Senoura, Jun Wasaki, Atsushi Hijikata, Masafumi Shionyu, Susumu Ito, Tsuyoshi Shirai
  • Organizer: 生物物理学会年会
  • Place of Presentation: 京都
• [Presentation] Crystal structure of novel enzyme 4-O-β-D-mannosyl-D glucose phosphorylase with substrate and product molecules (2013)
  • Author(s): Setsu Nakae, Shigeaki Ito, Mariko Higa, Takeshi Senoura, Jun Wasaki, Atsushi, Hijikata, Masafumi Shionyu, Susumu Ito Tsuyoshi Shirai
  • Organizer: AsCA'13
  • Place of Presentation: 香港
• [Presentation] ダイニンモータードメインのX線構造解析 (2013)
  • Author(s): 昆隆英、大山拓次、下-昆理恵子、須藤和夫、栗栖源嗣
  • Organizer: 第13回日本蛋白質科学会年会
  • Place of Presentation: 鳥取
• [Presentation] 核内受容体PPARδリガンド結合ドメインとパーシャルアゴニストJK122の複合体結晶構造 (2013)
  • Author(s): 大山拓次、中村仁美、春日淳一、宮地弘幸、楠木正巳
  • Organizer: 平成25年度日本生化学会関東支部例会
  • Place of Presentation: 山梨
• [Presentation] 核内受容体PPARγリガンド結合ドメインとスルホン酸含有新規パーシャルアゴニストの複合体結晶構造 (2013)
  • Author(s): 大山拓次、大橋雅生、宮地弘幸、楠木正巳
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 神戸
• [Presentation] 線菌Saccharopolyspora rectivirgula由来の耐熱性β-ガラクトシダーゼ酵素の結晶構造生物 (2012)
  • Author(s): 渡辺慎太郎、大山拓次、竹内耕平、中山亨、楠木正巳
  • Organizer: 第85回日本生化学会年会
  • Place of Presentation: 福岡国際会議場、マリンメッセ福岡
  • Year and Date: 2012-12-15
• [Presentation] Structural basis for the activation of the nuclear receptor, PPARgamma, by fatty acid-and serotonin metabolites (2012)
  • Author(s): Tsuyoshi Waku, Takuma Shiraki, Takuji Oyama, Clara Shinyu, Kosuke Morikawa
  • Organizer: 第85回日本生化学会年会
  • Place of Presentation: 福岡国際会議場、マリンメッセ福岡
  • Year and Date: 2012-12-15
• [Presentation] Thermoplasma acidophilum由来Cdc6/Orclとホモ4量体のGINSによるMCMとの相乗的な活性化 (2012)
  • Author(s): 尾木野弘実、石野園子、真柳浩太、大山拓次、白井剛、森川耿右、Gyri Teien Haugland、Nils-Kare Birkeland、石野良純
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場、マリンメッセ福岡
  • Year and Date: 2012-12-13
• [Presentation] モータータンパク質ダイニンに特徴的なストーク領域の構造研究 (2012)
  • Author(s): 西河洋祐、大山拓次、枝松正樹、豊嶋陽子、昆隆英、栗栖源嗣
  • Organizer: 平成24年度日本結晶学会年会
  • Place of Presentation: 東北大学片平キャンパス
  • Year and Date: 2012-10-25
• [Presentation] 放線菌Saccharopolyspora rectivirgula由来の耐熱性β-ガラクトシダーゼ野生型酵素の結晶構造解析 (2012)
  • Author(s): 渡辺慎太郎、大山拓次、竹内耕平、中山亨、楠木正巳
  • Organizer: 平成24年度日本結晶学会年会
  • Place of Presentation: 東北大学片平キャンパス
  • Year and Date: 2012-10-25
• [Presentation] 単粒子解析による複製関連複合体の制御機構の研究 (2012)
  • Author(s): 真柳浩太
  • Organizer: 遺伝学研究集会
  • Place of Presentation: 遺伝学研究所
  • Year and Date: 2012-10-03
• [Presentation] 新規セントロメア特異的ヒストン様複合体CENP-TWSXの構造機能解析 (2012)
  • Author(s): 西野達哉、竹内康造、Karen Gascoigne、鈴木應志、堀哲也、大山拓次、森川耿右、Iain Cheeseman、深川竜郎
  • Organizer: 第12回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場
  • Year and Date: 2012-06-21
• [Presentation] ダイニンモータードメインの2.8-Å結晶構造 (2012)
  • Author(s): 昆隆英、大山拓次、下一昆理恵子、須藤和夫、栗栖源嗣
  • Organizer: 第12回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場
  • Year and Date: 2012-06-20
• [Book] バイオインフォマティクス入門, (2015)
  • Author(s): 日本バイオインフォマティクス学編（白井剛 編集代表者）
  • Total Pages: 176
  • Publisher: 慶應義塾大学出版会
• [Book] Methods in Molecular Biology vol. 1200 (2014)
  • Author(s): Ogawa T, Shirai T
  • Total Pages: 613
  • Publisher: Springer
• [Book] 生命のビッグデータ利用の最前線 (2014)
  • Author(s): 辻 敏之, 白井 剛
  • Total Pages: 231
  • Publisher: シーエムシー出版
• [Book] Protein Engineering - Technology and Application (2013)
  • Author(s): Tomohisa Ogawa, Tsuyoshi Shirai
  • Total Pages: 22
  • Publisher: InTech
• [Patent(Industrial Property Rights)] 耐熱性ミスマッチエンドヌクレアーゼの利用方法 (2014)
  • Inventor(s): 上森隆司, 石野良純, 相良武宏, 石野園子, 山上健, 白井剛
  • Industrial Property Rights Holder: 上森隆司, 石野良純, 相良武宏, 石野園子, 山上健, 白井剛
  • Industrial Property Rights Type: 特許
  • Filing Date: 2014-09-11