Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers

Takashi Ozawa, Hironao Yamada, Takeshi Miyakawa, Ryota Morikawa, Sota Yagi, Satoshi Akanuma, Akihiko Yamagishi, Masako Takasu

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    Artificial creation of fibers utilizing proteins has been a target of bionanotechnology. Yagi et al. succeeded in designing artificial protein fibers using two types of proteins: LARFH and sulerythrin. Binding interfaces were designed for sulerythrin and LARFH by introducing mutations, and the fibrous structures were confirmed by atomic force microscopy. However, branching was observed in the fibrous structure, possibly because of non-specific interactions between the proteins. In this study, we analyzed the behavior and binding sites of sulerythrin mutants and LARFH mutants using coarse-grained molecular dynamics (MD) simulation. Binding simulations were performed for a system of one sulerythrin and one LARFH, and also of two sulerythrin molecules and four LARFH molecules. These results suggested that glutamic acids originally possessed by sulerythrin contribute to non-specific binding at sites other than the designed interfaces.

    Original languageEnglish
    Title of host publicationProceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
    PublisherAssociation for Computing Machinery
    Pages43-47
    Number of pages5
    ISBN (Electronic)9781450353410
    DOIs
    Publication statusPublished - 2018 Jan 18
    Event8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018 - Tokyo, Japan
    Duration: 2018 Jan 182018 Jan 20

    Other

    Other8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018
    CountryJapan
    CityTokyo
    Period18/1/1818/1/20

    Fingerprint

    Nanofibers
    Molecular dynamics
    Proteins
    Computer simulation
    Molecules
    Fibers
    Binding sites
    Atomic force microscopy
    Acids

    Keywords

    • Fibrosis
    • LARFH
    • MD simulation
    • Nanotechnology
    • Sulerythrin

    ASJC Scopus subject areas

    • Human-Computer Interaction
    • Computer Networks and Communications
    • Computer Vision and Pattern Recognition
    • Software

    Cite this

    Ozawa, T., Yamada, H., Miyakawa, T., Morikawa, R., Yagi, S., Akanuma, S., ... Takasu, M. (2018). Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. In Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018 (pp. 43-47). Association for Computing Machinery. https://doi.org/10.1145/3180382.3180390

    Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. / Ozawa, Takashi; Yamada, Hironao; Miyakawa, Takeshi; Morikawa, Ryota; Yagi, Sota; Akanuma, Satoshi; Yamagishi, Akihiko; Takasu, Masako.

    Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery, 2018. p. 43-47.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Ozawa, T, Yamada, H, Miyakawa, T, Morikawa, R, Yagi, S, Akanuma, S, Yamagishi, A & Takasu, M 2018, Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. in Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery, pp. 43-47, 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018, Tokyo, Japan, 18/1/18. https://doi.org/10.1145/3180382.3180390
    Ozawa T, Yamada H, Miyakawa T, Morikawa R, Yagi S, Akanuma S et al. Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. In Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery. 2018. p. 43-47 https://doi.org/10.1145/3180382.3180390
    Ozawa, Takashi ; Yamada, Hironao ; Miyakawa, Takeshi ; Morikawa, Ryota ; Yagi, Sota ; Akanuma, Satoshi ; Yamagishi, Akihiko ; Takasu, Masako. / Coarse-grained molecular dynamics simulation of sulerythrin and LARFH for producing protein nanofibers. Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2018. Association for Computing Machinery, 2018. pp. 43-47
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    AU - Yagi, Sota

    AU - Akanuma, Satoshi

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