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

• Project/Area Number: 25440023
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Kobe 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: ¥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)
• Keywords: protein 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.

Research Products

• [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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Organization of the multiaminoacyl-tRNA synthetase complex and the cotranslational protein folding (2015)
  • 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
  • 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 extracts (2014)
  • Author(s): Tokmakov AA
  • Journal Title: Frontiers in Microbiology Volume: v. 5 Pages: 295-295
  • DOI: 10.3389/fmicb.2014.00295
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Calcium signaling and meiotic exit at fertilization in Xenopus egg (2014)
  • 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
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Bioinformatics analysis and optimization of cell-free protein synthesis (2014)
  • 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
  • Peer Reviewed
• [Journal Article] Correlations between protein disorder and post-translational modifications in plants (2014)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Monitoring gene expression in a single Xenopus oocyte using multiple cytoplasmic collections and quantitative RT-PCR (2014)
  • 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
  • Peer Reviewed
• [Presentation] Apoptosis in Xenopus oocytes and eggs (2015)
  • 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
• [Presentation] Bioinformatics approach to identify physicochemical and structural properties accociated with successful cell-free protein synthesis (2015)
  • Author(s): Alexander Tokmakov
  • Organizer: 17th International Conference on Bioinformatics and Biotechnology
  • Place of Presentation: Marrakech, Morokko
  • Year and Date: 2015-04-08
• [Presentation] The presence of multiple sites of ubiquitination and SUMOylation is associated with increased cell-free production of soluble protein (2014)
  • 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
• [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
• [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
• [Presentation] Physiological relevance of frog egg apoptosis (2014)
  • 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
• [Presentation] mRNA degradation in apoptotic Xenopus eggs (2013)
  • 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
• [Presentation] Gene expression profiling in single Xenopus oocytes and eggs (2013)
  • 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
• [Presentation] Gene expression profiling in living Xenopus oocytes (2013)
  • Author(s): 3. Alexander Tokmakov, Takanori Hashimoto, Sho Iguchi, Tetsushi Iwasaki, Yasuo Fukami
  • Organizer: 86th Annual Meeting of JBS
  • Place of Presentation: Yokohama, Japan