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Systematic mutational analysis of a relationship between a protein's immunogenicity and aggregation tendency using Solubility Conttroling Peptide (SCP) tags

Research Project

Project/Area Number 18H02385
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43020:Structural biochemistry-related
Research InstitutionTokyo University of Agriculture and Technology

Principal Investigator

Kuroda Yutaka  東京農工大学, 工学(系)研究科(研究院), 教授 (10312240)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000)
Fiscal Year 2021: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2020: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2019: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2018: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000)
Keywords生物物理 / 免疫応答解析 / バイオテクノロジー / 免疫原性 / ウイルスタンパク質 / コロナ / 溶解性制御タグ / 免疫増強 / タンパク質 / 会合性の制御 / バイオインフォマティクス / デング
Outline of Final Research Achievements

We developed a technology to control protein aggregation by adding a short solubility-controlling peptide tag (SCP tag) to the termini of two model proteins, BPTI and ED3, using recombinant DNA technology. We found that an SCP tag consisting of 5 Ile not only oligomerized the proteins into soluble aggregates but also increased immunogenicity by more than 200-fold compared to that of the wild type.

Academic Significance and Societal Importance of the Research Achievements

凝集はタンパク質やペプチドの免疫原性に大きく影響を及ぼす因子であると従来から考えられてきた。しかし、タンパク質が形成する可溶性会合体の大きさや物性を適切に制御することが出来なかったため、凝集と免疫原性の関係を生化学的・物理化学的実験で検証することはなかった。本研究の学術的意義は、わずか5個のIleから成るSCPタグを付加することでモデルタンパク質の溶解性・凝集性を制御し、SCPタグによって会合させたタンパク質の免疫原性が飛躍的に向上するということである。社会的意義は、SCPタグがタンパク質を抗原とするサブユニットワクチンの可能性を大きく促進させた点である。

Report

(4 results)
  • 2021 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report

Research Products

(60 results)

All 2021 2020 2019 2018 Other

All Int'l Joint Research (7 results) Journal Article (15 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 15 results,  Open Access: 9 results) Presentation (35 results) (of which Int'l Joint Research: 2 results,  Invited: 7 results) Book (2 results) Remarks (1 results)

  • [Int'l Joint Research] チッタゴン大学・理学部(バングラデシュ)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] グラナダ大学・理学部(スペイン)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] モンペリエ大学・構造生化学研究センター(フランス)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] チッタゴン大学・理学部(バングラデシュ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] モンペリエ大学・構造生化学研究センター(フランス)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] チッタゴン大学・理学部(バングラデシュ)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] モンペリエ大学・構造生化学研究センター(フランス)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-192021

    • Author(s)
      Ando Shiho、Matsuzawa Yuki、Tsurui Hiromichi、Mizutani Tetsuya、Hall Damien、Kuroda Yutaka
    • Journal Title

      Scientific Reports

      Volume: 11(1) Pages: 6856-6856

    • DOI

      10.1038/s41598-021-86027-2

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Solution structure of Gaussia Luciferase with five disulfide bonds and identification of a putative coelenterazine binding cavity by heteronuclear NMR.2020

    • Author(s)
      N. Wu, N. Kobayashi, K. Tsuda, S. Unzai, T. Saotome, Y. Kuroda and T. Yamazaki.
    • Journal Title

      Scientific Reports

      Volume: 10 Pages: 20069-20069

    • DOI

      10.1038/s41598-020-76486-4

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A systematic mutational analysis identifies a 5‐residue proline tag that enhances the in vivo immunogenicity of a non‐immunogenic model protein2020

    • Author(s)
      Rahman Nafsoon、Islam Mohammad Monirul、Kibria Md. Golam、Unzai Satoru、Kuroda Yutaka
    • Journal Title

      FEBS Open Bio

      Volume: 10(10) Pages: 1947-1956

    • DOI

      10.1002/2211-5463.12941

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The immunogenicity of an anti-EGFR single domain antibody (VHH) is enhanced by misfolded amorphous aggregation but not by heat-induced aggregation2020

    • Author(s)
      Kibria Md. Golam、Akazawa-Ogawa Yoko、Rahman Nafsoon、Hagihara Yoshihisa、Kuroda Yutaka
    • Journal Title

      European Journal of Pharmaceutics and Biopharmaceutics

      Volume: 152 Pages: 164-174

    • DOI

      10.1016/j.ejpb.2020.05.006

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nanometer-Sized Aggregates Generated Using Short Solubility Controlling Peptide Tags Do Increase the In Vivo Immunogenicity of a Nonimmunogenic Protein2020

    • Author(s)
      Rahman Nafsoon、Islam Mohammad Monirul、Unzai Satoru、Miura Shiho、Kuroda Yutaka
    • Journal Title

      Molecular Pharmaceutics

      Volume: 17(5) Pages: 1629-1637

    • DOI

      10.1021/acs.molpharmaceut.0c00071

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Thermodynamic Analysis of Point Mutations Inhibiting High-Temperature Reversible Oligomerization of PDZ32020

    • Author(s)
      Saotome Tomonori、Mezaki Taichi、Brindha Subbaian、Unzai Satoru、Martinez Jose C.、Kidokoro Shun-ichi、Kuroda Yutaka
    • Journal Title

      Biophysical Journal

      Volume: 119(7) Pages: 1391-1401

    • DOI

      10.1016/j.bpj.2020.08.023

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Reversible oligomerization and reverse hydrophobic effect induced by isoleucine tags attached at the C-terminus of a simplified BPTI variant2020

    • Author(s)
      Shigeyoshi Nakamura, MD. Golam Kibria, Satoru Unzai, Yutaka Kuroda, Shun-ichi Kidokoro
    • Journal Title

      Biochemistry

      Volume: 59 Pages: 3660-3668

    • DOI

      10.1021/acs.biochem.0c00436

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Anti-Dengue ED3 Long-Term Immune Response With T-Cell Memory Generated Using Solubility Controlling Peptide Tags2020

    • Author(s)
      Islam Mohammad M.、Miura Shiho、Hasan Mohammad N.、Rahman Nafsoon、Kuroda Yutaka
    • Journal Title

      Frontiers in Immunology

      Volume: 11 Pages: 333-333

    • DOI

      10.3389/fimmu.2020.00333

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] How A Novel Scientific Concept Was Coined the “Molten Globule State”2020

    • Author(s)
      Kuroda Yutaka、Endo Shigeru、Nakamura Haruki
    • Journal Title

      Biomolecules

      Volume: 10 Pages: 269-269

    • DOI

      10.3390/biom10020269

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A novel caged Cookson‐type reagent toward a practical vitamin D derivatization method for mass spectrometric analyses2020

    • Author(s)
      Seki Masahiko、Sato Makoto、Takiwaki Masaki、Takahashi Koji、Kikutani Yoshikuni、Satoh Mamoru、Nomura Fumio、Kuroda Yutaka、Fukuzawa Seketsu
    • Journal Title

      Rapid Commun Mass Spectrom

      Volume: 34

    • DOI

      10.1002/rcm.8648

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Folding of the Ig-like domain of the envelope protein from dengue virus analyzed by high hydrostatic pressure NMR at a residue-level resolution2019

    • Author(s)
      Saotome Tomonori, Doret Maxime, Kulkarni R Manjiri, Yang Yin-Shan, Barthe Philippe, Kuroda Yutaka, Roumestand Christian
    • Journal Title

      Biomolecules

      Volume: 9(8) Pages: 309-309

    • DOI

      10.3390/biom9080309

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Misfolding of a Single Disulfide Bonded Globular Protein into a Low-Solubility Species Conformationally and Biophysically Distinct from the Native One2019

    • Author(s)
      Saotome Tomonori、Yamazaki Toshio、Kuroda Yutaka
    • Journal Title

      Biomolecules

      Volume: 9(6) Pages: 250-250

    • DOI

      10.3390/biom9060250

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Hydrophobic surface residues can stabilize a protein through improved water?protein interactions2019

    • Author(s)
      Islam Mohammad M.、Kobayashi Kei、Kidokoro Shun‐Ichi、Kuroda Yutaka
    • Journal Title

      The FEBS Journal

      Volume: 286(20) Pages: 4122-4134

    • DOI

      10.1111/febs.14941

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity2019

    • Author(s)
      Tambi Richa、Morimoto Gentaro、Kosuda Satoshi、Taiji Makoto、Kuroda Yutaka
    • Journal Title

      Scientific Reports

      Volume: 9(1) Pages: 2530-2530

    • DOI

      10.1038/s41598-018-38401-w

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Design and assessment of an active anti-epidermal growth factor receptor (EGFR) single chain variable fragment (ScFv) with improved solubility2019

    • Author(s)
      Nautiyal Kalpana、Kibria Md Golam、Akazawa-Ogawa Yoko、Hagihara Yoshihisa、Kuroda Yutaka
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 508(4) Pages: 1043-1049

    • DOI

      10.1016/j.bbrc.2018.11.170

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Presentation] ラテックス凝集法を用いた抗デング3 型ウイルス由来エンベロープタンパク質第3 ドメイン抗体の検出2020

    • Author(s)
      井上 絢惠、福谷 星、黒田 裕
    • Organizer
      第10回日本生物物理学会関東支部会
    • Related Report
      2020 Annual Research Report
  • [Presentation] PSD95-PDZ3 の熱変性過程で可逆的に形成された高温での可逆的なオリゴマーのリバースエンジニアリング2020

    • Author(s)
      Onchaiya Sawaros、早乙女 友規、城所 俊一、黒田 裕
    • Organizer
      第10回日本生物物理学会関東支部会
    • Related Report
      2020 Annual Research Report
  • [Presentation] デング熱ウィルスED3における高頻出アミノ酸変異箇所の効率的な予測手法の開発2020

    • Author(s)
      Xian Jingwen、黒谷 篤之、黒田 裕
    • Organizer
      第10回日本生物物理学会関東支部会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 格子モデルを用いたCOVID-19等伝染性ウイルスの感染拡大シミュレーション2020

    • Author(s)
      安東 紫帆、松沢 佑紀、黒田 裕
    • Organizer
      第10回日本生物物理学会関東支部会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 新型コロナウイルスの変異体予測モデルの開発2020

    • Author(s)
      Cheng ZhiRui、黒谷篤之、黒田裕
    • Organizer
      第10回日本生物物理学会関東支部会
    • Related Report
      2020 Annual Research Report
  • [Presentation] デング・エンベロープ蛋白質第3ドメインのミスフォールディングと凝集2020

    • Author(s)
      黒田 裕 、早乙女 友規
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 溶解性制御タグ(SCPタグ)を用いたタンパク質凝集体の形成速度の解析及びその制御法の開発2020

    • Author(s)
      Onchaiya Sawaros、Velmurugan Punitha、黒田裕
    • Organizer
      第9回日本生物物理学会関東支部会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Pictet-Spengler 反応を用いた抗EGFR-VHHのN末端特異的蛍光標識2020

    • Author(s)
      福谷 星、福沢 世傑、黒田 裕
    • Organizer
      第9回日本生物物理学会関東支部会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 静電相互作用により会合したデングED3タンパク質凝集体の物性と免疫原性の評価2020

    • Author(s)
      大川 真実、Rahman Nafsoon、三浦 史帆、黒田 裕
    • Organizer
      第9回日本生物物理学会関東支部会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Biophysical analysis of protein solubility and aggregation2019

    • Author(s)
      Kuroda Yutaka
    • Organizer
      International Powder and Nanotechnology Forum(IPNF) 2019
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Investigation on the relationship between cytotoxicity and amorphous oligomers2019

    • Author(s)
      Velmurugan Punitha, Aklima Jannatul, Ohta Yoshihiro, Kuroda Yutaka
    • Organizer
      第5回国立精神神経医療センター・東京農工大学合同シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] Biophysical studies of protein misfolding, solubility,and aggregation2019

    • Author(s)
      Yutaka Kuroda, Tomonori Saotome
    • Organizer
      The 19th KIAS(Korea Institute for Advanced Study) Conference on Protein Structure and Function
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Investigation on the relationship between cytotoxicity and amorphous oligomers2019

    • Author(s)
      Velmurugan Punitha, Aklima Jannatul, Ohta Yoshihiro, Kuroda Yutaka
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Nanometer scale sub-visible aggregates can enhance a protein's immunogenicity2019

    • Author(s)
      Rahman Nafsoon, Islam M Mohammad, Unzai Satoru, Kuroda Yutaka
    • Organizer
      第19回日本蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Biophysical and immunological study of natively folded and low soluble precipitate species of anti-EGFR single domain antibody (VHH)2019

    • Author(s)
      Kibria Md Golam, Akazawa-Ogawab Yoko, Hagihara Yoshihisa, Kuroda Yutaka
    • Organizer
      第19回日本蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 深層学習によるドメインリンカー予測の改良2019

    • Author(s)
      松沢 佑紀、黒田 裕
    • Organizer
      第19回日本蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Biophysical studies of a protein’s amorphous aggregation and its effect on immune response2019

    • Author(s)
      Kuroda Yutaka
    • Organizer
      BSBMB (Bangladesh Society for Biochemistry and Molecular Biology) Conference 2019 “Life Sciences in Achieving Sustainable Development Goals”
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 液液相分離の粗粒化モデル作成2019

    • Author(s)
      小原 真、河村 直樹、黒田 裕
    • Organizer
      第8回日本生物物理学会関東支部会
    • Related Report
      2018 Annual Research Report
  • [Presentation] DEN4ED3におけるプロ配列(pro region)付加によるジスルフィド結合の形成に関する解析2019

    • Author(s)
      山本 裕子、早乙女 友規、黒田 裕
    • Organizer
      第8回日本生物物理学会関東支部会
    • Related Report
      2018 Annual Research Report
  • [Presentation] BPTIをモデルタンパク質に用いた疎水性ペプチドタグの付加によるアモルファス会合体の細胞毒性2019

    • Author(s)
      前田 華子、Velmurugan Punitha, Aklima Jannatul, 太田 善浩、黒田 裕
    • Organizer
      第8回日本生物物理学会関東支部会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 疎水性の短いペプチドタグを付加したデングウイルス由来エンベロープタンパク質第3ドメインの免疫原性及び物性の解析2019

    • Author(s)
      塩飽 祐佳里、三浦 史帆、黒田 裕
    • Organizer
      第8回日本生物物理学会関東支部会
    • Related Report
      2018 Annual Research Report
  • [Presentation] SCPタグを付加したBPTIの溶解傾向性におけるアミノ酸の寄与の探究2019

    • Author(s)
      髙木 開生、黒田 裕
    • Organizer
      第8回日本生物物理学会関東支部会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Nanometer scale sub-visible aggregates can enhance a protein’s immunogenicity2018

    • Author(s)
      Rahman Nafsoon, Islam M Mohammad, Kuroda Yutaka
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 短いペプチドタグを付加したデングウイルス由来エンベロープタンパク質第3ドメインにおける会合状態および免疫原性の評価2018

    • Author(s)
      三浦 史帆、Islam M Mohammad、黒田 裕
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Design and development of a soludle single-chain variable fragment (ScFc biological activity)2018

    • Author(s)
      Kibria Md Golam, Nautiyal Kalpana, Akazawa-Ogawa Yoko, Hagihara Yoshihisa, Kuroda Yutaka
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 深層学習を用いたドメインリンカー予測2018

    • Author(s)
      松沢 佑紀、河村 直樹、黒田 裕
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 格子モデルを用いたタンパク質凝集のシミュレーション2018

    • Author(s)
      小原 真、河村 直樹、黒田 裕
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 生物情報科学的手法を用いた蛋白質の構造・物性解析とその実験的検証2018

    • Author(s)
      黒田 裕 (座長:渡辺元)
    • Organizer
      第161回日本獣医学会学術集会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 蛋白質立体構造解析のフロンティア2018

    • Author(s)
      黒田 裕(オーガナイザー:城所 俊一)
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 蛋白質・ペプチドの凝集と膜のないオルガネラ2018

    • Author(s)
      黒田 裕(オーガナイザー:永井 義隆)
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 蛋白質のアモルファス凝集の生物物理学的研究2018

    • Author(s)
      黒田 裕
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] K4型デングウイルス由来エンベロープ第3ドメインの封入体の巻き戻しから生じる構造の異なる二種類のコンホマーに関する考察2018

    • Author(s)
      早乙女 友規、山崎 俊夫、黒田 裕
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 短いペプチドタグを付加したデングウイルス由来エンベロープ蛋白質ドメイン3における会合状態および免疫原性の評価2018

    • Author(s)
      三浦 史帆、Islam M Mohammad、黒田 裕
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Enhancing Solubility of Anti-EGFR Single chain Antibody Fragment (ScFV) via Solubility Enhancing Peptides (SEP) Tags2018

    • Author(s)
      Nautiyal Kalpana, Kibria Md.Golam, Akazawa-Ogawa Yoko, Hagihara Yoshihisa, Kuroda Yutaka
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Biophysical characterization of an insoluble species formed by a chemically intact single disulfide bonded BPTI2018

    • Author(s)
      Velmurugan Punitha, Kuroda Yutaka
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
  • [Book] 化学工業「タンパク質表面電荷が溶解性に及ぼす影響の格子モデル解析」2019

    • Author(s)
      小原 真、黒田 裕
    • Publisher
      化学工業社
    • Related Report
      2019 Annual Research Report
  • [Book] タンパク質のアモルファス凝集と溶解性―基礎研究からバイオ産業・創薬研究への応用まで―2019

    • Author(s)
      黒田 裕、有坂 文雄(監修)
    • Total Pages
      283
    • Publisher
      シーエムシー出版
    • ISBN
      9784781313979
    • Related Report
      2018 Annual Research Report
  • [Remarks] ~ロックダウンによるコロナウイルス感染拡大抑制効果の相対的な予測に向けて~

    • URL

      https://www.tuat.ac.jp/outline/disclosure/pressrelease/2020/20200818_01.html

    • Related Report
      2020 Annual Research Report

URL: 

Published: 2018-04-23   Modified: 2023-01-30  

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