Comprehensive creation of antibody-like ligands for human proteomics

• Project/Area Number: 15H05372
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Chemical biology
• Research Institution: University of Yamanashi (2016-2017); National Institute of Advanced Industrial Science and Technology (2015)
• Principal Investigator: KAWAKAMI Takashi 山梨大学, 大学院総合研究部, 助教 (60638881)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥23,920,000 (Direct Cost: ¥18,400,000、Indirect Cost: ¥5,520,000); Fiscal Year 2017: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000); Fiscal Year 2016: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000); Fiscal Year 2015: ¥11,440,000 (Direct Cost: ¥8,800,000、Indirect Cost: ¥2,640,000)
• Keywords: プロテオミクス / HUPEX / ヒト腕型ロボット / 無細胞タンパク質合成系 / 部位特異的ビオチン化 / cDNAクローン / PUREシステム / in vitro virus / 無細胞翻訳系 / 環状Nアルキルペプチド / 汎用ヒト腕型ロボット / mRNAディスプレイ / cDNAディスプレイ / 抗体 / ペプトイド / DNLC-MS/MS / Nアルキルペプチド

Outline of Final Research Achievements

By integrating cyclic peptide ligand creation using PURE system and mRNA display with HUPEX to prepare immobilized human proteins from its encoding cDNA clones, we successfully created novel cyclic peptide ligands targeted to the human proteins in a full cell-free format. By combining the system with humanoid robot system, human protein-binding ligands created fully automatically were successfully applied to proteomic analysis.

Research Products

• [Journal Article] Peptide Selection against Reactive Small Molecular Probes for Protein Imaging and Opto-genetics by Using the DIVERSE Screening System (2017)
  • Author(s): Mizuki Yamamoto, Hiroki Suzuki, Tomohiro Iwabuchi, Yu Shimizu, Takashi Kawakami
  • Journal Title: Peptide Science Volume: 印刷中
  • Peer Reviewed
• [Journal Article] Directed Evolution of a Cyclized Peptoid-Peptide Chimera against a Cell-Free Expressed Protein and Proteomic Profiling of the Interacting Proteins to Create a Protein-Protein Interaction Inhibitor (2016)
  • Author(s): Takashi Kawakami, Koji Ogawa, Tomohisa Hatta, Naoki Goshima, and Tohru Natsume
  • Journal Title: ACS Chemical Biology Volume: 11 Issue: 6 Pages: 1569-77
  • DOI: 10.1021/acschembio.5b01014
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] De Novo Creation of Non-enzymatically Covalent-labeling Peptide Tags for Protein Imaging by Using the DIVERSE System (2016)
  • Author(s): Miya Kurata, Naoko Yanada, Koichiro Ikai, Daiki Sakamoto, Takashi Kawakami
  • Journal Title: Peptide Science Volume: 53 Pages: 227-228
  • Peer Reviewed
• [Journal Article] Site-specific Labeling of Peptide-tagged Proteins with Nano-sized Fluorescent Probes in Living Cells for Single-molecule Imaging (2016)
  • Author(s): Naoko Yanada, Miya Kurata, Daiki Sakamoto, Koichiro Ikai, Takashi Kawakami
  • Journal Title: Peptide Science Volume: 53 Pages: 207-208
  • Peer Reviewed
• [Journal Article] DIVERSE System: De Novo Creation of Peptide Tags for Non-enzymatic Covalent Labeling by In Vitro Evolution for Protein Imaging Inside Living Cells (2015)
  • Author(s): Takashi Kawakami, Koji Ogawa, Naoki Goshima, and Tohru Natsume
  • Journal Title: Chemistry & Biology Volume: 22 Issue: 12 Pages: 1671-1679
  • DOI: 10.1016/j.chembiol.2015.10.016
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] In vitro display evolution of cyclized peptidomimetics targeted to a chemically synthesized amyloid beta protein dimer (2015)
  • Author(s): Takashi Kawakami, Kazuma Murakami, Daiki Sakamoto, Mizuho Hanaki, Tohru Natsume, and Kazuhiro Irie
  • Journal Title: Peptide Science Volume: 52 Pages: 323-324
  • Peer Reviewed
• [Journal Article] Post-translational modification mapping of collagen that binds to HSP47 by directed ligand evolution and DNLC mass spectrometry (2015)
  • Author(s): Takashi Kawakami, Shinya Ito, Naoki Goshima, Kazuhiro Nagata, and Tohru Natsume
  • Journal Title: Peptide Science Volume: 52 Pages: 321-322
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Peptide Selection against Reactive Small Molecular Probes for Protein Imaging and Opto-genetics by Using the DIVERSE Screening System (2017)
  • Author(s): 山本美月、鈴木宏輝、岩渕智宏、川上隆史
  • Organizer: 第54回ペプチド討論会
• [Presentation] ChemistryからBiologyへの展開-DIVERSEスクリーニングシステムの開発とバイオイメージングへの応用- (2017)
  • Author(s): 川上隆史
  • Organizer: 日本化学会第97春季年会
  • Place of Presentation: 慶応義塾大学（神奈川県横浜市）
  • Invited
• [Presentation] DIVERSEシステムを用いた蛋白質ラベリング用ペプチドタグ創製とバイオイメージングへの応用 (2017)
  • Author(s): 川上隆史
  • Organizer: 第７回「産と学をつなぐSENRIの会」
  • Place of Presentation: 千里ライフサイエンスセンタービル（大阪府大阪市）
  • Invited
• [Presentation] 試験管内分子進化法を用いたPPI阻害環状Nアルキルペプチド化合物の創製 (2016)
  • Author(s): 川上隆史
  • Organizer: 新学術領域研究「天然物ケミカルバイオロジー」地区ミニシンポジウム～天然物ケミカルバイオロジーの更なる発展を目指して～
  • Place of Presentation: 京都大学（京都府京都市）
  • Year and Date: 2016-02-23
  • Invited
• [Presentation] De Novo Creation of Non-enzymatically Covalent-labeling Peptide Tags for Protein Imaging by Using the DIVERSE System (2016)
  • Author(s): 倉田みや、簗田奈央子、猪飼航一郎、坂本大樹、川上隆史
  • Organizer: 日本ペプチド学会第53回ペプチド討論会
  • Place of Presentation: 京都テルサ（京都府京都市）
• [Presentation] Site-specific Labeling of Peptide-tagged Proteins with Nano-sized Fluorescent Probes in Living Cells for Single-molecule Imaging (2016)
  • Author(s): 簗田奈央子、倉田みや、坂本大樹、猪飼航一郎、川上隆史
  • Organizer: 日本ペプチド学会第53回ペプチド討論会
  • Place of Presentation: 京都テルサ（京都府京都市）
• [Presentation] Directed evolution of antibody-like peptides for proteomics (2015)
  • Author(s): Takashi Kawakami, Naoki Goshima, and Tohru Natsume
  • Organizer: The 2015 International Chemical Congress of Pacific Basin Societies
  • Place of Presentation: Honolulu (USA)
  • Year and Date: 2015-12-15
  • Int'l Joint Research
• [Presentation] 無細胞分子進化法と超高感度質量分析を用いた翻訳後修飾の網羅的解析 (2015)
  • Author(s): 川上隆史、伊藤進也、五島直樹、永田和宏、夏目徹
  • Organizer: 日本ペプチド学会第５２回ペプチド討論会
  • Place of Presentation: 平塚中央公民館（神奈川県平塚市）
  • Year and Date: 2015-11-16
• [Presentation] アミロイドβ二量体を標的とする非天然型環状ペプチドの試験管内分子進化 (2015)
  • Author(s): 川上隆史、村上一馬、阪本大樹、花木瑞穂、夏目徹、入江一浩
  • Organizer: 日本ペプチド学会第５２回ペプチド討論会
  • Place of Presentation: 平塚中央公民館（神奈川県平塚市）
  • Year and Date: 2015-11-16
• [Presentation] 進化分子工学と有機合成化学を基盤とするペプチドツール創製システムの構築 (2015)
  • Author(s): 川上隆史
  • Organizer: BioJapan2015 World Business Forum
  • Place of Presentation: パシフィコ横山（神奈川県横浜市）
  • Year and Date: 2015-10-15
  • Int'l Joint Research / Invited
• [Presentation] タンパク質ラベリング用ペプチドタグの進化分子工学的創製システムの構築 (2015)
  • Author(s): 川上隆史、五島直樹、夏目徹
  • Organizer: 日本ケミカルバイオロジー学会第１０回年会
  • Place of Presentation: 東北大学（宮城県仙台市）
  • Year and Date: 2015-06-10
• [Presentation] プロテオミクスアプローチによるタンパク質間相互作用阻害剤の同定 (2015)
  • Author(s): 川上隆史、五島直樹、夏目徹
  • Organizer: 「天然物ケミカルバイオロジー～分子標的と活性制御～」第８回公開シンポジウム
  • Place of Presentation: 東北大学（宮城県仙台市）
  • Year and Date: 2015-06-08
• [Book] ２種類の人工塩基を有するDNAアプタマー (2018)
  • Author(s): 山本美月、川上隆史
  • Publisher: 羊土社
• [Book] 細胞膜透過性ペプチド創製を指向したPUREシステムとmRNAディスプレイ法による大環状Nアルキルペプチドの超高速スクリーニング (2017)
  • Author(s): 山本美月、鈴木宏輝、岩渕智宏、清水優、川上隆史
  • Publisher: 技術情報協会
• [Remarks] 山梨大学 生命環境学部 生命工学科 川上研究室のホームページ
  • URL: http://www.bt.yamanashi.ac.jp/modules/kenkyu/index.php?content_id=20
• [Remarks]
  • URL: http://www.molprof.jp/~kawakami/
• [Remarks]
  • URL: http://researchmap.jp/takakawa/