Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation

T. Ishioka, H. Yamada, T. Miyakawa, R. Morikawa, Satoshi Akanuma, A. Yamagishi, M. Takasu

    研究成果: Conference contribution

    抄録

    Proteins, which incorporate charged and hydrophobic amino acid residues, are useful as a material of nanotechnology. Among these proteins, IPMDH (3-isopropylmalate dehydrogenase), which has thermal stability, has potential as a material of nanofiber. In this study, we performed coarse-grained molecular dynamics simulation of IPMDH using MARTINI force fields, and we investigated the orientation for the binding of IPMDH. In simulation, we analyzed wild type of IPMDH and the mutated IPMDH proteins, where 13, 20, 27, 332, 335 and 338th amino acid residues are replaced by lysine residues which have positive charge and by glutamic acid residues which have negative charge. Since the binding of mutated IPMDH is advantageous compared with the binding of wild type for one orientation, we suggest that the Coulomb interaction for the binding of IPMDH is important.

    本文言語English
    ホスト出版物のタイトルInternational Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016
    出版社American Institute of Physics Inc.
    1790
    ISBN(電子版)9780735414549
    DOI
    出版ステータスPublished - 2016 12 6
    イベントInternational Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016 - Athens, Greece
    継続期間: 2016 3 172016 3 20

    Other

    OtherInternational Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016
    CountryGreece
    CityAthens
    Period16/3/1716/3/20

    ASJC Scopus subject areas

    • Physics and Astronomy(all)

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