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Crystallization and crystallography of proteins at in vivo salt concentrations

Research Project

Project/Area Number 18K04960
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 30010:Crystal engineering-related
Research InstitutionThe University of Tokushima

Principal Investigator

SUZUKI Yoshihisa  徳島大学, 大学院社会産業理工学研究部(理工学域), 准教授 (60325248)

Co-Investigator(Kenkyū-buntansha) 佐藤 正英  金沢大学, 総合メディア基盤センター, 教授 (20306533)
佐崎 元  北海道大学, 低温科学研究所, 教授 (60261509)
Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2019: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywordsニワトリ卵白リゾチーム / グルコースイソメラーゼ / 液液相分離 / 平均二乗変位 / 沈殿剤フリー / 生理食塩水 / 分子クラウディング / 平均二乗偏差 / 斜方晶系結晶 / 正方晶系結晶 / 生体内 / タンパク質 / 結晶化 / 結晶構造解析
Outline of Final Research Achievements

We have clarified significant structure changes in three-dimensional structure of protein molecules in crystals from different growth conditions. We studied effects of the difference in precipitant condition on the structure, and published papers on the result. In addition, in dilute precipitant conditions, liquid-liquid phase separation frequently occurred during centrifugal concentration of solutions. In the dense liquid phase after the separation, nucleation and growth of crystals occurred very rapidly. Growth rates of obtained crystals in the dense liquid were at least an order of magnitude faster than those in conventional salting-out conditions. In spite of such very rapid processes, maximum resolution limits of obtained crystals were very high (less than 0.1 nm, for instance).

Academic Significance and Societal Importance of the Research Achievements

結晶化条件の違いによって、タンパク質分子の構造が有意に違うということは、創薬等で、生体内の条件下での結晶化が必要とされることを意味する。病因タンパク質の3次元立体分子構造をもとにした特効薬の開発、いわゆるStructrue based drug designでは、そのプロセスで0.15 nmの回折分解能を持つ高品質結晶が要求される。しかし、本研究において、生理食塩水程度の塩濃度における結晶の構造解析、その分解能よりもはるかに大きな構造変化があることが分かった。
本研究では、塩濃度の違いによって明白な構造変化を明らかにし、かつ従来であれば結晶化できないような低塩濃度における結晶化手法を確立した。

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (23 results)

All 2021 2020 2019 2018

All Journal Article (12 results) (of which Peer Reviewed: 11 results,  Open Access: 3 results) Presentation (11 results) (of which Int'l Joint Research: 2 results)

  • [Journal Article] Effect of the Interaction Length on Clusters Formed by Spherical One-Patch Particles on Flat Planes2021

    • Author(s)
      Sato Masahide
    • Journal Title

      Langmuir

      Volume: 37 Issue: 14 Pages: 4213-4221

    • DOI

      10.1021/acs.langmuir.1c00102

    • NAID

      120007016746

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effect of Patch Area and Interaction Length on Clusters and Structures Formed by One-Patch Particles in Thin Systems2020

    • Author(s)
      Sato Masahide
    • Journal Title

      ACS Omega

      Volume: 5 Issue: 44 Pages: 28812-28822

    • DOI

      10.1021/acsomega.0c04159

    • NAID

      120006942658

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Highly purified glucose isomerase crystals under microgravity conditions grow as fast as those on the ground do2020

    • Author(s)
      Yoshihisa Suzuki, Ai Ninomiya, Seijiro Fukuyama, Taro Shimaoka, Masae Nagai, Koji Inaka, Shin-ichiro Yanagiya, Takehiko Sone, Shingo Wachi, Yasutomo Arai, Katsuo Tsukamoto
    • Journal Title

      ChemRxiv.

      Volume: preprint Pages: 1-12

    • DOI

      10.26434/chemrxiv.11808504.v1

    • Related Report
      2019 Research-status Report
  • [Journal Article] A novel handling-free method of mounting single protein crystals for synchrotron structure analyses at room temperature2019

    • Author(s)
      Yoshihisa Suzuki, Kumi Torii, Koji Inaka, Takahisa Fujiwara, Hiroaki Tanaka and Yasutomo Arai
    • Journal Title

      The Review of Scientific Instruments

      Volume: 90 Issue: 5

    • DOI

      10.1063/1.5070122

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Self-Assembly Formed by Spherical Patchy Particles with Long-Range Attraction2019

    • Author(s)
      Masahide Sato
    • Journal Title

      Journal of the Physical Society of Japan

      Volume: 88 Issue: 10 Pages: 104801-104801

    • DOI

      10.7566/jpsj.88.104801

    • NAID

      120006716906

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Effect of the Surface Diffusion and Evaporation of Impurities on Step Bunching Induced by Impurities2019

    • Author(s)
      Masahide Sato
    • Journal Title

      Journal of the Physical Society of Japan

      Volume: 88 Issue: 11 Pages: 114801-114801

    • DOI

      10.7566/jpsj.88.114801

    • NAID

      120006731732

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Very low nucleation rates of glucose isomerase crystals under microgravity in the International Space Station2019

    • Author(s)
      Yoshihisa Suzuki, Takahisa Fujiwara, Katsuo Tsukamoto, Seijiro Fukuyama, Taro Shimaoka, Kazuma Tsuchiya, Ai Ninomiya, Yumiko Murakumo, Akiho Ikeuchi, Hitomi Minamizono, Tomokazu Yamazaki, Takehiko Sone, Tetsuya Sakashita, Masae Nagai and Yasutomo Arai
    • Journal Title

      Crystals

      Volume: 9 Issue: 2 Pages: 90-90

    • DOI

      10.3390/cryst9020090

    • NAID

      120006937617

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effect of density change at crystallization on a one-dimensional heat balance equation at solid-liquid interface2019

    • Author(s)
      Atsushi Mori, Masahide Sato and Yoshihisa Suzuki
    • Journal Title

      Japanese Journal of Applied Physics, Part 1 (Regular Papers & Short Notes)

      Volume: 58 Issue: 4 Pages: 045506-045506

    • DOI

      10.7567/1347-4065/ab0707

    • NAID

      120006605141

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Precipitant-free lysozyme crystals grown by centrifugal concentration reveal structural changes2018

    • Author(s)
      Yoshihisa Suzuki, Hideaki Tsuge, Hironori Hondoh, Yusuke Kato, Yuta Uehara, Nobuo Maita, Kohei Hosokawa and Shoko Ueta
    • Journal Title

      Crystal Growth & Design

      Volume: 18 Issue: 8 Pages: 4226-4229

    • DOI

      10.1021/acs.cgd.8b00326

    • NAID

      120006652020

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Dependence of Convection Flow Rates on Gravity around Growing Hen Egg-White Lysozyme Crystals2018

    • Author(s)
      Yoshihisa Suzuki, Takahisa Fujiwara, Tomohiro Shiomoto, Tetsuya Toyooka, Daidoh Nakahashi, Katsuo Tsukamoto and Yuko Inatomi
    • Journal Title

      International Journal of Microgravity Science and Application

      Volume: 35

    • NAID

      130007768946

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Two-dimensional structures formed in a binary system of DNA nanoparticles with a short-range interaction potential2018

    • Author(s)
      Sato Masahide
    • Journal Title

      Japanese Journal of Applied Physics

      Volume: 57 Issue: 12 Pages: 125002-125002

    • DOI

      10.7567/jjap.57.125002

    • NAID

      120006534715

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Effect of evaporation on step bunching induced by impurities2018

    • Author(s)
      Sato Masahide
    • Journal Title

      Physical Review E

      Volume: 97 Issue: 6

    • DOI

      10.1103/physreve.97.062801

    • NAID

      120006484645

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Presentation] 分子クラウディング様条件下におけるタンパク質の結晶化および結晶構造解析2021

    • Author(s)
      鈴木 良尚
    • Organizer
      日本物理学会第76回年次大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] タンパク質結晶の成長と不純物効果2020

    • Author(s)
      鈴木良尚、塚本勝男、二宮愛、福山誠二郎、島岡太郎、永井正恵、三浦均、藤原貴久、伊中浩治、曽根武彦、和知慎吾、吉崎泉、荒井康智
    • Organizer
      第49回 結晶成長国内会議
    • Related Report
      2020 Annual Research Report
  • [Presentation] グルコースイソメラーゼ結晶のステップ前進速度に対する不純物効果2020

    • Author(s)
      森下 桃花, 柳谷 伸一郎, 鈴木 良尚
    • Organizer
      第49回 結晶成長国内会議
    • Related Report
      2020 Annual Research Report
  • [Presentation] 液液相分離後の濃厚相で核生成するグルコースイソメラーゼ結晶のその場観察2020

    • Author(s)
      池光 直人, 鈴木 良尚
    • Organizer
      第49回 結晶成長国内会議
    • Related Report
      2020 Annual Research Report
  • [Presentation] 生理食塩水中におけるタンパク質の結晶構造2020

    • Author(s)
      鈴木 良尚, 坂井 隆志
    • Organizer
      第49回 結晶成長国内会議
    • Related Report
      2020 Annual Research Report
  • [Presentation] Precipitant-free crystallization of glucose isomerase simply by concentration in a cryoprotectant solution2019

    • Author(s)
      Yoshihisa Suzuki and Nobuo Maita
    • Organizer
      The 19th International Conference on Crystal Growth and Epitaxy
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] 結晶化条件によって変化するタンパク質の分子構造2019

    • Author(s)
      鈴木 良尚, 津下 英明, 本同 宏成, 加藤 有介, 真板 宣夫, 植原 悠太, 伊中 浩治
    • Organizer
      第48回結晶成長国内会議
    • Related Report
      2019 Research-status Report
  • [Presentation] Precipitant-free crystallization of proteins2018

    • Author(s)
      Yoshihisa Suzuki, Takahisa Fujiwara, Hideaki Tsuge, Hironori Hondoh, Yusuke Kato, Yuta Uehara, Nobuo Maita, Kohei Hosokawa, Shoko Ueta
    • Organizer
      International Symposium & School on Crystal Growth Fundamentals
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 濃縮するだけで実現するタンパク質結晶化2018

    • Author(s)
      鈴木 良尚, 藤原 貴久, 津下 英明, 本同 宏成, 加藤 有介, 植原 悠太, 真板 宣夫, 細川 晃平, 上田 昭子
    • Organizer
      第47回結晶成長国内会議
    • Related Report
      2018 Research-status Report
  • [Presentation] 常温におけるタンパク質結晶の放射光X線構造解析2018

    • Author(s)
      土谷 一眞, 鈴木 良尚, 伊中 浩治, 田仲 広明, 永井 正恵
    • Organizer
      第47回結晶成長国内会議
    • Related Report
      2018 Research-status Report
  • [Presentation] グルコースイソメラーゼ結晶のスパイラル成長丘におけるステップのその場観察2018

    • Author(s)
      二宮 愛, 鈴木 良尚, 藤原 貴久, 柳谷 伸一郎, 荒井 康智, 永井 正恵
    • Organizer
      第47回結晶成長国内会議
    • Related Report
      2018 Research-status Report

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Published: 2018-04-23   Modified: 2022-01-27  

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