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New insights into protein folding based on bioinformatics analysis of cell-free protein synthesis

Research Project

Project/Area Number 25440023
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Structural biochemistry
Research InstitutionKobe University

Principal Investigator

TOKMAKOV ALEXANDER  神戸大学, 遺伝子実験センター, 研究員 (20301278)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2013: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywordsprotein folding / cell-free synthesis / bioinformatics / intrinsic disorder
Outline of Final Research Achievements

In the present study, a bioinformatics approach for identification of multiple physicochemical and structural properties associated with cell-free soluble protein expression was developed. It is based on categorical data analysis of correlations between experimentally observed expression scores and multiple features of amino acid sequences calculated/predicted by bioinformatics. Using this approach, we found that protein disorder is associated with low propensity for detectable cell-free protein expression and elevated ratio of soluble expression. These tendencies are rooted in the distinct features of intrinsically disordered regions, such as low hydrophobicity, elevated surface accessibility and high abundance of sequence motifs for proteolytic degradation. We also found that the eukaryotic PTMs, such as phosphorylation, glycosylation and acetylation, display a clear preference for occurrence in disordered regions of plant proteins, whereas methylation tends to avoid disorder.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (16 results)

All 2015 2014 2013

All Journal Article (7 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 7 results,  Open Access: 5 results,  Acknowledgement Compliant: 3 results) Presentation (9 results)

  • [Journal Article] Content of intrinsic disorder influences the outcome of cell-free protein synthesis.2015

    • Author(s)
      Tokmakov AA, Kurotani A, Ikeda M, Terazawa Y, Shirouzu M, Stefanov V, Sakurai T, Yokoyama S.
    • Journal Title

      Scientific Reports

      Volume: v. 5 Issue: 1 Pages: 14079-14079

    • DOI

      10.1038/srep14079

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Organization of the multiaminoacyl-tRNA synthetase complex and the cotranslational protein folding2015

    • Author(s)
      Berezovsky IN, Zheng Z, Kurotani A, Tokmakov AA, Kurochkin IV.
    • Journal Title

      Protein Science

      Volume: 24 Issue: 9 Pages: 1475-1485

    • DOI

      10.1002/pro.2735

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification of multiple physicochemical and structural properties associated with soluble expression of eukaryotic proteins in cell-free bacterial extracts2014

    • Author(s)
      Tokmakov AA
    • Journal Title

      Frontiers in Microbiology

      Volume: v. 5 Pages: 295-295

    • DOI

      10.3389/fmicb.2014.00295

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Calcium signaling and meiotic exit at fertilization in Xenopus egg2014

    • Author(s)
      Tokmakov AA, Stefanov VE, Iwasaki T, Sato K, Fukami Y.
    • Journal Title

      International Journal of Molecular Sciences (IJMS)

      Volume: v. 15 (10) Issue: 10 Pages: 18659-18676

    • DOI

      10.3390/ijms151018659

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Bioinformatics analysis and optimization of cell-free protein synthesis2014

    • Author(s)
      2. Tokmakov AA, Kurotani A, Shirouzu M, Fukami Y, Yokoyama S.
    • Journal Title

      Methods Mol Biol

      Volume: v. 1118 Pages: 17-33

    • DOI

      10.1007/978-1-62703-782-2_2

    • ISBN
      9781627037815, 9781627037822
    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Correlations between protein disorder and post-translational modifications in plants2014

    • Author(s)
      3. Kurotani A, Tokmakov AA, Kuroda Y, Fukami Y, Shinozaki K, Sakurai T.
    • Journal Title

      Bioinformatics

      Volume: v. 30 Issue: 8 Pages: 1095-1103

    • DOI

      10.1093/bioinformatics/btt762

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Monitoring gene expression in a single Xenopus oocyte using multiple cytoplasmic collections and quantitative RT-PCR2014

    • Author(s)
      1. Tokmakov AA, Hashimoto T, Hasegawa Y, Iguchi S, Iwasaki T, Fukami Y.
    • Journal Title

      FEBS Journal

      Volume: v. 281 Issue: 1 Pages: 104-114

    • DOI

      10.1111/febs.12576

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] Apoptosis in Xenopus oocytes and eggs2015

    • Author(s)
      Alexander Tokmakov, Sho Iguchi, Liang Zhu, Tetsushi Iwasaki, Shinji Kamada
    • Organizer
      86th Annual Meeting of Zoological Society of Japan
    • Place of Presentation
      新潟コンベンションセンター朱鷺メッセ ,新潟市、新潟県
    • Year and Date
      2015-09-17
    • Related Report
      2015 Annual Research Report
  • [Presentation] Bioinformatics approach to identify physicochemical and structural properties accociated with successful cell-free protein synthesis2015

    • Author(s)
      Alexander Tokmakov
    • Organizer
      17th International Conference on Bioinformatics and Biotechnology
    • Place of Presentation
      Marrakech, Morokko
    • Year and Date
      2015-04-08
    • Related Report
      2015 Annual Research Report
  • [Presentation] The presence of multiple sites of ubiquitination and SUMOylation is associated with increased cell-free production of soluble protein2014

    • Author(s)
      Alexander Tokmakov, Atsushi Kurotani, Mikako Shirouzu, Yasuo Fukami, Shigeyuki Yokoyama
    • Organizer
      Ubiquitin and UBLs: At the crossroads from chromatin to protein EMBO Conference
    • Place of Presentation
      Buenos Aires, Argentina
    • Year and Date
      2014-10-19 – 2014-10-24
    • Related Report
      2014 Research-status Report
  • [Presentation] Apoptotic degradation of mature ovulated eggs: Why eggs die by apoptosis in biological species with external fertilization.2014

    • Author(s)
      Alexander A. Tokmakov, Sho Iguchi, Tetsushi Iwasaki, Yasuo Fukami
    • Organizer
      The 85th Annual Meeting of the Zoological Society of Japan
    • Place of Presentation
      Tohoku University, Sendai, Japan
    • Year and Date
      2014-09-11
    • Related Report
      2014 Research-status Report
  • [Presentation] Bioinformatics analysis of cell-free protein synthesis.2014

    • Author(s)
      Alexander Tokmakov
    • Organizer
      ICPAC 2014 International Conference on Pure and Applied Chemistry
    • Place of Presentation
      Flic en Flac, Mauritius
    • Year and Date
      2014-06-23 – 2014-06-27
    • Related Report
      2014 Research-status Report
  • [Presentation] Physiological relevance of frog egg apoptosis2014

    • Author(s)
      Alexander A. Tokmakov, Sho Iguchi, Tetsushi Iwasaki, Yasuo Fukami
    • Organizer
      The 47th Annual Meeting of Japanese Society of Developmental Biologists
    • Place of Presentation
      Winc Aichi, Nagoya, Japan
    • Year and Date
      2014-05-27 – 2014-05-30
    • Related Report
      2014 Research-status Report
  • [Presentation] mRNA degradation in apoptotic Xenopus eggs2013

    • Author(s)
      1. Alexander A. Tokmakov, Takanori Hashimoto, Yushi Hasegawa, Sho Iguchi, Tetsushi Iwasaki and Yasuo Fukami
    • Organizer
      Cold Spring Harbor symposium on Eukaryotic mRNA processing
    • Place of Presentation
      Cold Spring Harbor, New York, USA
    • Related Report
      2013 Research-status Report
  • [Presentation] Gene expression profiling in single Xenopus oocytes and eggs2013

    • Author(s)
      2. Alexander A. Tokmakov, Takanori Hashimoto, Yushi Hasegawa, Sho Iguchi, Tetsushi Iwasaki and Yasuo Fukami
    • Organizer
      ISPROF 2013, 1st International Symposium on Profiling
    • Place of Presentation
      Costa da Caparica, Lisbon, Portugal
    • Related Report
      2013 Research-status Report
  • [Presentation] Gene expression profiling in living Xenopus oocytes2013

    • Author(s)
      3. Alexander Tokmakov, Takanori Hashimoto, Sho Iguchi, Tetsushi Iwasaki, Yasuo Fukami
    • Organizer
      86th Annual Meeting of JBS
    • Place of Presentation
      Yokohama, Japan
    • Related Report
      2013 Research-status Report

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Published: 2014-07-25   Modified: 2019-07-29  

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