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

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

    Abstract

    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.

    Original languageEnglish
    Title of host publicationInternational Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016
    PublisherAmerican Institute of Physics Inc.
    Volume1790
    ISBN (Electronic)9780735414549
    DOIs
    Publication statusPublished - 2016 Dec 6
    EventInternational Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016 - Athens, Greece
    Duration: 2016 Mar 172016 Mar 20

    Other

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

    Fingerprint

    dehydrogenases
    molecular dynamics
    proteins
    simulation
    amino acids
    glutamic acid
    lysine
    nanotechnology
    field theory (physics)
    thermal stability

    Keywords

    • Coarse-grained model
    • Coulomb interaction
    • Hydrophobic effect
    • Molecular dynamics
    • Protein fibers

    ASJC Scopus subject areas

    • Physics and Astronomy(all)

    Cite this

    Ishioka, T., Yamada, H., Miyakawa, T., Morikawa, R., Akanuma, S., Yamagishi, A., & Takasu, M. (2016). Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. In International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016 (Vol. 1790). [020023] American Institute of Physics Inc.. https://doi.org/10.1063/1.4968649

    Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. / Ishioka, T.; Yamada, H.; Miyakawa, T.; Morikawa, R.; Akanuma, Satoshi; Yamagishi, A.; Takasu, M.

    International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016. Vol. 1790 American Institute of Physics Inc., 2016. 020023.

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

    Ishioka, T, Yamada, H, Miyakawa, T, Morikawa, R, Akanuma, S, Yamagishi, A & Takasu, M 2016, Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. in International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016. vol. 1790, 020023, American Institute of Physics Inc., International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016, Athens, Greece, 16/3/17. https://doi.org/10.1063/1.4968649
    Ishioka T, Yamada H, Miyakawa T, Morikawa R, Akanuma S, Yamagishi A et al. Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. In International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016. Vol. 1790. American Institute of Physics Inc. 2016. 020023 https://doi.org/10.1063/1.4968649
    Ishioka, T. ; Yamada, H. ; Miyakawa, T. ; Morikawa, R. ; Akanuma, Satoshi ; Yamagishi, A. ; Takasu, M. / Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016. Vol. 1790 American Institute of Physics Inc., 2016.
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    abstract = "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.",
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    AU - Miyakawa, T.

    AU - Morikawa, R.

    AU - Akanuma, Satoshi

    AU - Yamagishi, A.

    AU - Takasu, M.

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    AB - 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.

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