Updated on 2024/02/27

写真a

 
OTA Motonori
 
Organization
Graduate School of Informatics Department of Complex Systems Science 2 Professor
Graduate School
Graduate School of Information Science
Graduate School of Informatics
Undergraduate School
School of Informatics Department of Natural Informatics
Title
Professor
Contact information
メールアドレス

Degree 1

  1. 博士（理学） （ 1996.10   早稲田大学 ） 

To the head of Degree.▲

Research Areas 2

  1. Life Science / Biophysics  / Theoretical biology, Bioinformatics

  2. Informatics / Life, health and medical informatics  / Bioinformatics

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Research History 5

  1. 東京工業大学　学術国際情報センター　助教授

    2002.4 - 2008.3

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    Country：Japan

  2. 国立遺伝学研究所　DDBJ・生命情報研究センター　助手

    1996.8 - 2002.3

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    Country：Japan

  3. 日本学術振興会　特別研究員（DC2）

    1996.4 - 1996.7

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    Country：Japan

  4. 蛋白工学研究所　研究員

    1994.4 - 1995.3

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    Country：Japan

  5. 東燃（株）総合研究所　研究員

    1990.4 - 1994.3

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    Country：Japan

To the head of Research History.▲

Education 1

  1. Waseda University

    1994.4 - 1996.10

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    Country： Japan

To the head of Education.▲
 

Papers 61

  1. Dual-wield NTPases: a novel protein family mined from AlphaFold protein structure database Reviewed International journal

    K. Sakuma, R, Koike, M. Ota

    Prot. Sci.   Vol. in press   2024

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  2. Elastic network model reveals distinct flexibilities of capping proteins bound to CARMIL and twinfilin-tail Reviewed International journal

    Koike, R; Ota, M

    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS   Vol. 92 ( 1 ) page： 37 - 43   2024.1

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Proteins: Structure, Function and Bioinformatics  

    Capping protein (CP) binds to the barbed end of an actin-filament and inhibits its elongation. CARMIL binds CP and dissociates it from the barbed end of the actin-filament. The binding of CARMIL peptide alters the flexibility of CP, which is considered to facilitate the dissociation. Twinfilin also binds to CP through its C-terminal tail. The complex structures of the CP/twinfilin-tail (TW-tail) peptide indicate that the binding sites of CARMIL and TW-tail overlap. However, TW-tail binding does not facilitate the dissociation of CP from the barbed end. We extensively investigated the flexibilities of CP in the CP/TW-tail or CP/CARMIL complexes using an elastic network model and concluded that TW-tail binding does not alter the flexibility of CP. Our extensive analysis also highlighted that the strong contacts of peptides with the two domains of CP, that is, the CP-L and CP-S domains, are key to changing the flexibilities of CP. CARMIL peptides can interact strongly with both of the domains, while TW-tail peptides exclusively interact with the CP-S domain because the binding site of TW-tail on CP relatively shifts to the CP-S domain compared with that of CP/CARMIL. This result supports our hypothesis that the dissociation of CP from the barbed end is regulated by the flexibility of CP.

    DOI： 10.1002/prot.26560

    Web of Science

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  3. Prediction of chaperonin GroE substrates using small structural patterns of proteins Reviewed International journal

    Minami Shintaro, Niwa Tatsuya, Uemura Eri, Koike Ryotaro, Taguchi Hideki, Ota Motonori

    FEBS OPEN BIO   Vol. 13 ( 4 ) page： 779 - 794   2023.4

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    Authorship：Last author,　Corresponding author   Language：English   Publisher：FEBS Open Bio  

    Molecular chaperones are indispensable proteins that assist the folding of aggregation-prone proteins into their functional native states, thereby maintaining organized cellular systems. Two of the best-characterized chaperones are the Escherichia coli chaperonins GroEL and GroES (GroE), for which in vivo obligate substrates have been identified by proteome-wide experiments. These substrates comprise various proteins but exhibit remarkable structural features. They include a number of α/β proteins, particularly those adopting the TIM β/α barrel fold. This observation led us to speculate that GroE obligate substrates share a structural motif. Based on this hypothesis, we exhaustively compared substrate structures with the MICAN alignment tool, which detects common structural patterns while ignoring the connectivity or orientation of secondary structural elements. We selected four (or five) substructures with hydrophobic indices that were mostly included in substrates and excluded in others, and developed a GroE obligate substrate discriminator. The substructures are structurally similar and superimposable on the 2-layer 2α4β sandwich, the most popular protein substructure, implying that targeting this structural pattern is a useful strategy for GroE to assist numerous proteins. Seventeen false positives predicted by our methods were experimentally examined using GroE-depleted cells, and 9 proteins were confirmed to be novel GroE obligate substrates. Together, these results demonstrate the utility of our common substructure hypothesis and prediction method.

    DOI： 10.1002/2211-5463.13590

    Web of Science

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  4. How AlphaFold2 predicts conditionally folding regions annotated in an intrinsically disordered protein database Reviewed International journal

    H. Anbo, K. Sakuma, S. Fukuchi, M. Ota

    Biology   Vol. 12   page： 182   2023.1

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.3390/biology12020182

  5. Classification of proteins inducing liquid-liquid phase separation: sequential, structural and functional characterization Invited Reviewed International journal

    Ozawa Yuhei, Anbo Hiroto, Ota Motonori, Fukuchi Satoshi

    JOURNAL OF BIOCHEMISTRY     2022.12

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  6. Structures and mechanisms of actin ATP hydrolysis Reviewed International journal

    Kanematsu Y., Narita A., Oda T., Koike R., Ota M., Takano Y., Moritsugu K., Fujiwara I., Tanaka K., Komatsu H., Nagae T., Watanabe N., Iwasa M., Maéda Y., Takeda S.

    Proceedings of the National Academy of Sciences of the United States of America   Vol. 119 ( 43 ) page： e2122641119   2022.10

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Proceedings of the National Academy of Sciences of the United States of America  

    The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and the filamentous F-form, which drive organelle transport and cell motility. This mechanical work is driven by the ATPase activity at the catalytic site in the F-form. For deeper understanding of the actin cellular functions, the reaction mechanism must be elucidated. Here, we show that a single actin molecule is trapped in the F-form by fragmin domain-1 binding and present their crystal structures in the ATP analog-, ADP-Pi-, and ADP-bound forms, at 1.15-Å resolutions. The G-to-F conformational transition shifts the side chains of Gln137 and His161, which relocate four water molecules including W1 (attacking water) and W2 (helping water) to facilitate the hydrolysis. By applying quantum mechanics/molecular mechanics calculations to the structures, we have revealed a consistent and comprehensive reaction path of ATP hydrolysis by the F-form actin. The reaction path consists of four steps: 1) W1 and W2 rotations; 2) PG–O3B bond cleavage; 3) four concomitant events: W1–PO32 formation, OH2 and proton cleavage, nucleophilic attack by the OH2 against PG, and the abstracted proton transfer; and 4) proton relocation that stabilizes the ADP-Pi–bound F-form actin. The mechanism explains the slow rate of ATP hydrolysis by actin and the irreversibility of the hydrolysis reaction. While the catalytic strategy of actin ATP hydrolysis is essentially the same as those of motor proteins like myosin, the process after the hydrolysis is distinct and discussed in terms of Pi release, F-form destabilization, and global conformational changes.

    DOI： 10.1073/pnas.2122641119

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  7. Evaluating cepharanthine analogues as natural drugs against SARS-CoV-2 Reviewed

    FEBS OPEN BIO   Vol. 12 ( 1 ) page： 285 - 294   2021.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/2211-5463.13337

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  8. Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins Invited Reviewed

    Hijikata Atsushi, Shionyu Clara, Nakae Setsu, Shionyu Masafumi, Ota Motonori, Kanaya Shigehiko, Shirai Tsuyoshi

    Biophys. Physicobiol.   Vol. 18 ( 0 ) page： 226 - 240   2021.10

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：一般社団法人 日本生物物理学会  

    <p>More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of <i>in silico</i> and <i>in vitro</i> screenings for drug repurposing, there is only a limited number of drugs had been successfully authorized by drug regulation organizations. Although many approved drugs and natural compounds, which exhibited antiviral activity <i>in vitro</i>, were considered potential drugs against COVID-19, a further multidisciplinary investigation is required for understanding the mechanisms underlying the antiviral effects of the drugs.</p>

    DOI： 10.2142/biophysico.bppb-v18.025

    Web of Science

  9. Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail Reviewed

    Takeda Shuichi, Koike Ryotaro, Fujiwara Ikuko, Narita Akihiro, Miyata Makoto, Ota Motonori, Maeda Yuichiro

    J. Mol. Biol.   Vol. 433 ( 9 ) page： 166891   2021.4

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Journal of Molecular Biology  

    Twinfilin is a conserved actin regulator that interacts with actin capping protein (CP) via C terminus residues (TWtail) that exhibits sequence similarity with the CP interaction (CPI) motif of CARMIL. Here we report the crystal structure of TWtail in complex with CP. Our structure showed that although TWtail and CARMIL CPI bind CP to an overlapping surface via their middle regions, they exhibit different CP-binding modes at both termini. Consequently, TWtail and CARMIL CPI restrict the CP in distinct conformations of open and closed forms, respectively. Interestingly, V-1, which targets CP away from the TWtail binding site, also favors the open-form CP. Consistently, TWtail forms a stable ternary complex with CP and V-1, a striking contrast to CARMIL CPI, which rapidly dissociates V-1 from CP. Our results demonstrate that TWtail is a unique CP-binding motif that regulates CP in a manner distinct from CARMIL CPI.

    DOI： 10.1016/j.jmb.2021.166891

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  10. Crystal structure of human V-1 in the apo form Reviewed

    S. Takeda, R. Koike, T. Nagae, I. Fujiwara, A. Narita, Y. Maéda, M. Ota

    Acta. Cryst. F   Vol. 77 ( Pt 1 ) page： 13 - 21   2021.1

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    Language：Japanese   Publishing type：Research paper (scientific journal)  

    DOI： 10.1107/S2053230X20016829

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  11. Knowledge-based Modeling of SARS-CoV-2 Proteins and Predicting its Potential Drugs Invited Reviewed

    HIJIKATA Atsushi, SHIONYU-MITSUYAMA Clara, NAKAE Setsu, SHIONYU Masafumi, OTA Motonori, KANAYA Shigehiko, SHIRAI Tsuyoshi

    Seibutsu Butsuri   Vol. 61 ( 2 ) page： 102 - 106   2021

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    Language：Japanese   Publishing type：Research paper (other academic)   Publisher：The Biophysical Society of Japan General Incorporated Association  

    <p>The novel coronavirus disease (COVID-19) pandemic has emerged in late 2019 and rapidly spread all over the world. In order to assist structure-based discovery efforts for repurposing drugs against the infectious disease, we constructed homology models of SARS-CoV-2 proteins. We identified several potential drugs by comparing the ligand molecules in the template structures with approved or experimental drugs and compounds of natural drugs, including carfilzomib, sinefungin, tecadenoson, and trabodenoson, that would be further investigated for their potential for treating COVID-19.</p>

    DOI： 10.2142/biophys.61.102

    CiNii Research

  12. Knowledge-based strutural models of SARS-CoV-2 proteins and their complexes with potential drugs Reviewed

    A. Hijikata, C. Shionyu-Mitsuyama, S. Nakae, M. Shionyu, M. Ota, S. Kanaya, T. Shirai

    FEBS Lett.   Vol. 594   page： 1960 - 1973   2020.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/1873-3468.13806

  13. All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins Reviewed

    R. Koike, M. Ota

    Biophys. Physicobiol.   ( 16 ) page： 280-286   2019.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： doi: 10.2142/biophysico.16.0_280

  14. Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins Reviewed

    R. Koike, M. Amano, K. Kaibuchi, M. Ota

    Protein Sci.   Vol. 29   page： 564-571   2019.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/pro.3789

  15. MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers Reviewed

    S. Minami, K. Sawada, M. Ota, G. Chikenji

    Bioinformatics   Vol. 34   page： 3324-3331   2018.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/bioinformatics/bty369

  16. Using 1HN amide temperature coefficients to define intrinsically disordered regions: An alternative NMR method Reviewed

    H. Okazaki, N. Matsuo, T. Tenno, N. Goda, Y. Shigemitsu, M. Ota, H. Hiroaki

    Protein Sci.   Vol. 27   page： 1821-1830   2018.8

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/pro.3485

  17. Discovery of Cryoprotective Activity in Human Genome-Derived Intrinsically Disordered Proteins Reviewed

    N. Matsuo, N. Goda, K. Shimizu, S. Fukuchi, M. Ota, H. Hiroaki

    Int. J. Mol. Sci.   Vol. 19   page： 401   2018.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.3390/ijms19020401

  18. Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding Reviewed

    E. Uemura, T. Niwa, S. Minami, K. Takemoto, S. Fukuchi, K. Machida, H. Imataka, T. Ueda, M. Ota, H. Taguchi

    Sci. Rep.   Vol. 8   page： 678   2018.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/s41598-017-18977-5

  19. Structural changes of homodimers in the PDB Reviewed

    R. Koike, T. Amemiya, T. Horii, M. Ota

    J. Str. Biol.     page： in press   2018

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.jsb.2017.12.004

  20. Rules for connectivity of secondary structure elements of proteins: Two-layer αβ sandwiches Reviewed

    S. Minami, G. Chikenji, M. Ota

    Prot. Sci.   Vol. 26   page： 2257-2267   2017.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/pro.3285

  21. Itinerary profiling to analyze a large number of protein-folding trajectories Reviewed

    M. Ota, M. Ikeguchi, A. Kidera

    Biophys. Physicobiol.   Vol. 13   page： 295-304   2016.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： doi.org/10.2142/biophysico.13.0_295

  22. Interface property responsible for effective interactions of protean segments: Intrinsically disordered regions that undergo disorder-to-order transitions upon binding Reviewed

    D. Shaji, T. Amemiya, R. Koike R, M. Ota

    BBRC   Vol. 478   page： 123-127   2016.9

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： doi: 10.1016/j.bbrc.2016.07.082

  23. Profile comparison revealed deviation from structural constraint at the positively selected sites Reviewed

    H. Oda , M. Ota, H. Toh

    Biosystems   Vol. 147   page： 67-77   2016.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： doi: 10.1016/j.biosystems.2016.07.007

  24. Multiple-localization and hub proteins Reviewed

    M. Ota, H. Gonja, R. Koike, S. Fukuchi

    PLoS ONE   Vol. 11   page： e0156455   2016.6

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： doi: 10.1371/journal.pone.0156455

  25. Comprehensive analysis of motions in molecular dynamics trajectories of the actin capping protein and its inhibitor complexes Reviewed

    R. Koike, S. Takeda, Y. Maéda, M. Ota

    Proteins   Vol. 84   page： 948-956   2016.4

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： doi: 10.1002/prot.25043

  26. Investigation of the fatty acid transporter-encoding genes SLC27A3 and SLC27A4 in autism Reviewed

    M. Maekawa, Y. Iwayama, T. Ohnishi, M. Toyoshima, C. Shimamoto, Y. Hisano, T. Toyota, S. Balan, H. Matsuzaki, Y. Iwata, S. Takagai, K. Yamada, M. Ota, S. Fukuchi, Y. Okada, W. Akamatsu, M. Tsujii, N. Kojima, Y. Owada, H. Okano, N. Mori, T. Yoshikawa

    Sci. Rep.   Vol. 5   page： 16239   2015.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： doi:10.1038/srep16239

  27. Domain-motion enhanced (DoME) model for efficient conformational sampling of multi-domain proteins Reviewed

    C. Kobayashi, Y. Matsunaga, R. Koike, M. Ota, Y. Sugita

    J. Phys. Chem. B   Vol. 119   page： 14584-14593   2015.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： doi: 10.1021/acs.jpcb.5b07668

  28. A method for systematic assessment of intrinsically disordered protein regions by NMR Reviewed

    N. Goda, K. Shimizu, Y. Kuwahara, T. Noguchi, T. Ikegami, M. Ota, H. Hiroaki

    Int. J. Mol. Sci.   Vol. 16   page： 15743-15760   2015.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.3390/ijms160715743

  29. Hierarchical domain-motion analysis of conformational changes in Sarcoplasmic Reticulum Ca2+-ATPase Reviewed

    C. Kobayashi, R. Koike, M. Ota, Y. Sugita

    Proteins   Vol. 83   page： 746-756   2015.4

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/prot.24763

  30. An optimized Npro-based method for the expression and purification of intrinsically disordered proteins for an NMR study Reviewed

    N. Goda, N. Matsuo, T. Tenno, S. Ishino, Y. Ishino, S. Fukuchi, M. Ota, H. Hiroaki

    IDP   Vol. 3   page： 1-6   2015.2

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1080/21690707.2015.1011004

  31. Hierarchical description and extensive classification of protein structural changes by Motion Tree Reviewed

    R. Koike, M. Ota, A. Kidera

    J. Mol. Biol.   Vol. 426   page： 752-762   2014.2

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.jmb.2013.10.034

  32. IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners Reviewed

    S. Fukuchi, T. Amemiya, S. Sakamoto, Y. Nobe, K. Hosoda, Y. Kado, SD. Murakami, R. Koike, H. Hiroaki, M. Ota

    Nucleic Acids Res.   Vol. 42   page： D320-D325   2014.1

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  33. Exon resequencing of H3K9 methyltransferase complex genes, EHMT1, EHMT2 and WIZ, in Japanese autism subjects Reviewed

    S. Balan, Y. Iwayama, M. Maekawa, T. Toyota, T. Ohnishi, M. Toyoshima, C. Shimamoto, K. Esaki, K. Yamada, Y. Iwata, K. Suzuki, M. Ide, M. Ota, S. Fukuchi, M. Tsujii, N. Mori, Y. Shinkai, T. Yoshikawa

    Molecular Autism     page： in the press   2014

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  34. Accidental interaction between PDZ domains and diclofenac revealed by NMR-assisted virtual screening Reviewed

    T. Tenno, N. Goda, Y. Umetsu, M. Ota, K. Kinoshita, H. Hiroaki

    Molecules   Vol. 18   page： 9567-9581   2013.8

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  35. Substrate-shielding and hydrolytic reaction in hydrolases Reviewed

    Y. Kanematsu, R. Koike, T. Amemiya, M. Ota

      Vol. 81   page： 926-932   2013.2

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  36. An assignment of intrinsically disordered regions of proteins based on NMR structures Reviewed

    M. Ota, R. Koike, T. Amemiya, T. Tenno, P. R. Romero, H. Hiroaki, A. K. Dunker, S. Fukuchi

    J. Str. Biol.   Vol. 181   page： 29-36   2013.1

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  37. Influence of structural symmetry on protein dynamics Reviewed

    Y. Matsunaga, R. Koike, M. Ota, J. Tame, A. Kidera

    PLos One   Vol. 7   page： e50011   2012.11

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  38. A nobel biclustering approach with iterative optimization to analyze gene expression data Reviewed

    S. Sutheworapong, M. Ota, H. Ohta, K. Kinoshita

    Adv. Appl. Bioinform. Chem.   Vol. 5   page： 23-59   2012.9

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  39. SCPC: A method to structurally compare protein complexes

    R. Koike, M. Ota

    Bioinformatics     page： in press   2012.2

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  40. PSCDB: a database for protein structural change upon ligand binding

    T. Amemiya, R. Koike, A. Kidera, M. Ota

    Nucleic Acids Res.     page： in press   2012

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  41. IDEAL: intrinsically disordered proteins with extensive annotations and literature

    S. Fukuchi, S. Sakamoto, Y. Nobe, SD. Murakami, T. Amemiya, K. Hosoda, R. Koike, H. Hiroaki, M. Ota

    Nucleic Acids Res.     page： in press   2012

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    Language：English   Publishing type：Research paper (scientific journal)  

  42. SAHG, a comprehensive database of predicted structures of all human proteins Reviewed

    C. Motono, J. Nakata, R. Koike, K. Shimizu, M. Shirota, T. Amemiya, K. Tomii, N. Nagano, N. Sakaya, K. Misoo, M, Sato, A. Kidera, H. Hiroaki, T. Shirai, K. Kinoshita, T. Noguchi, M. Ota

    Nucleic Acids Res.   Vol. 39   page： D487   2011

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  43. Cover and spacer insertions: small non-hydrophobic accessories that assist protein oligomerization

    H. Nishi, R. Koike, M. Ota

    Proteins   Vol. 79   page： 2372-2379   2011

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  44. Actin capping protein and its inhibitor CARMIL: how intrinsically disordered regions function Reviewed

    S. Takeda, R. Koike, Y. Nitanai, S. Minakata, Y. Maéda, M. Ota

    Phys. Biol.   Vol. 8   page： 035005   2011

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  45. Remarkable improvement in the heat stability of CutA1 from Escherichia coli by rational protein design Reviewed

    Y. Matsuura, M. Ota, T. Tanaka, M. Takehira, K. Ogasahara, B. Bagautdinov, N. Kunishima, K. Yutani

    J. Biochem.   Vol. 148   page： 449-458   2010

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  46. Amino acid substitutions at protein-protein interfaces that modulate the oligomeric state Reviewed

    H. Nishi, M. Ota

    Proteins   Vol. 78   page： 1563-1574   2010

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  47. Two distinct mechanisms for actin capping proteinregulationTwo distinct mechanisms for actin capping proteinregulation- steric and allosteric inhibitionsteric and allosteric inhibition Reviewed

    S. Takeda, S. Minakata, R. Koike, I. Kawahata, A. Narita, M. Kitazawa, M. Ota, T.Yamakuni, Y. Maéda, Y. Nitanai

    PLos Biol.   Vol. 8   page： e1000416   2010

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  48. Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold Reviewed

    R. Koike, A. Kidera, M. Ota

    Protein Sci.   Vol. 18   page： 2060-2066   2009

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  49. An evaluation of minimal cellular functions to sustain a bacterial cell Reviewed

    Y. Azuma, M. Ota

    BMC Syst. Biol.   Vol. 3   page： 111   2009

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  50. An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories Reviewed

    H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang

    BMC Bioinformatics   Vol. 9   page： 344   2008

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  51. Protein structural change upon ligand binding correlates with enzymatic reaction mechanism Reviewed

    R. Koike, T. Amemiya, M. Ota, A. Kidera

    J. Mol. Biol.   Vol. 379   page： 397-401   2008

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  52. Unfolding pathways of goat α-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories Reviewed

    T. Oroguchi, M. Ikeguchi, M. Ota, K. Kuwajima and A. Kidera

    J. Mol. Biol.   Vol. 371   page： 1354-64   2007

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  53. Enhanced partial order curve comparison over multiple protein folding trajectories Reviewed

    H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang

    Comput. Syst. Bioinformatics. Conf.   Vol. 6   page： 299-310   2007

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    Language：English   Publishing type：Research paper (scientific journal)  

  54. A hyperthermophilic protein acquires function at the cost of stability Reviewed

    A. Mukaiyama, M. Haruki, M. Ota, Y. Koga, K. Takano and S. Kanaya

    Biochemistry   Vol. 24   page： 12673-12679   2006

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    Language：English   Publishing type：Research paper (scientific journal)  

  55. Stabilization of E. coli ribonuclease HI by the 'stability profile of mutant protein' (SPMP)-inspired random and non-random mutagenesis Reviewed

    M. Haruki, Y. Saito, M. Ota, K. Nishikawa, S. Kanaya

    J. Biotech.   Vol. 25   page： 512-522   2006

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    Language：English   Publishing type：Research paper (scientific journal)  

  56. Design of λ Cro fold: solution structure of a monomeric variant of the de novo protein Reviewed

    Y. Isogai, Y. Ito, T. Ikeya, Y. Shiro, M. Ota

    J. Mol. Biol.   Vol. 354   page： 801-814   2005

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  57. P-cats: Prediction of catalytic residues in proteins from the tertiary structures Reviewed

    K. Kinoshita and M. Ota

    Bioinformatics   Vol. 21   page： 3570-3571   2005

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  58. Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry Reviewed

    Y. Asada, M. Sawano, K. Ogasahara, J. Nakamura, M. Ota, C. Kuroishi, M. Sugahara, K. Yutani, N. Kunishima

    J Biochem (Tokyo)   Vol. 138   page： 343-353   2005

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  59. Phylogeny of protein-folding trajectories reveals a unique pathway to native structure Reviewed

    M. Ota, M. Ikeguchi and A. Kidera

    Proc. Natl. Acad. Sci. USA   Vol. 101   page： 17658-17663   2004

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  60. Integrative annotation of 21,037 human genes validated by full-length cDNA clones Reviewed

    T. Imanishi et al.

    PLoS. Biol.   Vol. 2   page： E162   2004

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  61. The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus Reviewed

    Y. Hioki, K. Ogasahara K, S. Lee, J. Ma, M. Ishida, Y. Yamagata, Y. Matsuura, M. Ota, M. Ikeguchi, S. Kuramitsu, K. Yutani

    Eur. J. Biochem.   Vol. 271   page： 2624-2635   2004

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Books 3

  1. Computational Methods to Predict Intrinsically Disordered Regions and Functional Regions in Them

    Anbo H., Ota M., Fukuchi S.

    Methods in Molecular Biology  2023 

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    Language：English

    Intrinsically disordered regions (IDRs) are protein regions that do not adopt fixed tertiary structures. Since these regions lack ordered three-dimensional structures, they should be excluded from the target portions of homology modeling. IDRs can be predicted from the amino acid sequences, because their amino acid compositions are different from that of the structured domains. This chapter provides a review of the prediction methods of IDRs and a case study of IDR prediction.

    DOI： 10.1007/978-1-0716-2974-1_13

    Scopus

    PubMed

  2. Protein Structural Changes Based on Structural Comparison

    Koike R., Ota M.

    Practical Guide to Life Science Databases  2022.1  （ ISBN:9789811658112 ）

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    Advances in structural biology have provided a wealth of information on protein structures. In many proteins, multiple structures under distinct functional states are available. The comparison of such structures reveals structural changes during the transition between the states, for example, those from ligand-free to -bound states. These structural changes are important for understanding the molecular mechanism of protein function. Currently, a number of computational methods have been developed to compare distinct structural states of the same protein and describe protein structural changes. The resulting structural changes are stored in databases. After a brief introduction of pre-existing methods and databases, we introduce Motion Tree, which illustrates various structural changes using a tree diagram and provides an explanation of how to use Motion Tree. We also introduce PSCDB, which presents structural changes for 837 proteins including homodimers. Structural changes are classified into seven categories based on the types of motions and bound ligands. PSCDB is available via the Internet.

    DOI： 10.1007/978-981-16-5812-9_8

    Scopus

  3. ドロプレット形成のデータベースと予測（相分離生物学の全貌　白木賢太郎編）

    太田元規，福地佐斗志（ Role： Contributor）

    東京化学同人  2020.11 

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    Total pages：402   Responsible for pages：363-367   Language：Japanese Book type：Scholarly book

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KAKENHI (Grants-in-Aid for Scientific Research) 1

  1. verification of the back-door model for actin phasphate release

    Grant number：22K06172  2022.4 - 2025.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

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    Authorship：Coinvestigator(s) 

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Industrial property rights 1

  1. タンパク質凍結保存用保護剤

    法人名大,産業技術総合研究所

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    Date applied：2015.1

    Announcement no：WO 2015/125501  Date announced：2015.8

    Country of applicant：Foreign country   Country of acquisition：Foreign country

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Teaching Experience (On-campus) 30

  1. 複雑系科学特論1

    2023

  2. 情報システムとしての自然１：生きる

    2023

  3. インフォマティックス４

    2023

  4. シミュレーション・サイエンス２

    2023

  5. 物質情報学10

    2023

  6. Introduction to Biophysics Ib

    2021

  7. First Year Seminar A

    2021

  8. Large-scale Complex Systems Computation 2

    2021

  9. Bioinformatics 1

    2021

  10. Physical and Life Science Informatics 3

    2021

  11. Bioinformatics 2

    2021

  12. Complex Systems Sciences 1

    2021

  13. Complex Systems Exercise 4

    2021

  14. Physical and Life Science Informatics 10

    2021

  15. Simulation Science 2

    2021

  16. Informatics 4

    2021

  17. Nature as Information System 1:Life

    2021

  18. First Year Seminar A

    2020

  19. Introduction to Biophysics Ib

    2020

  20. Complex Systems Exercise 4

    2020

  21. Physical and Life Science Informatics 10

    2020

  22. Physical and Life Science Informatics 3

    2020

  23. Simulation Science 2

    2020

  24. Informatics 4

    2020

  25. Nature as Information System 1:Life

    2020

  26. バイオインフォマティクス特論2

    2020

  27. バイオインフォマティクス特論1

    2020

  28. 複雑系科学特論1

    2020

  29. 計算科学フロンティア

    2020

  30. 大規模複雑系計算特論２

    2020

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