Analysis of interactions between green fluorescent protein and silicon substrates using molecular dynamics simulations

Katsuhiko Nishiyama, Takanobu Watanabe, Tadatsugu Hoshino, Iwao Ohdomari

    Research output: Contribution to journalArticle

    13 Citations (Scopus)

    Abstract

    We have performed a series of molecular dynamics (MD) simulations on interactions between green fluorescent protein (GFP) and Si substrates. The results show that GFP adsorbs directly on the hydrophobic substrate, and via water molecules on the hydrophilic substrate. The adsorption-induced changes in the conformation of GFP are smaller on the hydrophilic substrate than on the hydrophobic substrate. On the other hand, the dynamic atom motions in GFP are larger on the hydrophobic substrate than on the hydrophilic substrate. In order to prevent the denaturation of proteins caused by immobilization on a substrate, the Si surface should be prepared from the viewpoints of both conformation and dynamic atom motions.

    Original languageEnglish
    Pages (from-to)8210-8215
    Number of pages6
    JournalJapanese Journal of Applied Physics, Part 1: Regular Papers and Short Notes and Review Papers
    Volume44
    Issue number11
    DOIs
    Publication statusPublished - 2005 Nov 9

    Fingerprint

    Molecular dynamics
    molecular dynamics
    proteins
    Proteins
    Silicon
    Computer simulation
    silicon
    Substrates
    simulation
    interactions
    Conformations
    Atoms
    Denaturation
    biopolymer denaturation
    immobilization
    atoms
    Adsorption
    Molecules
    adsorption
    water

    Keywords

    • Biomedical application
    • GFP
    • Green fluorescent protein
    • MD
    • Molecular dynamics simulations
    • Nanostructure
    • Protein chip
    • Si substrates

    ASJC Scopus subject areas

    • Physics and Astronomy (miscellaneous)

    Cite this

    Analysis of interactions between green fluorescent protein and silicon substrates using molecular dynamics simulations. / Nishiyama, Katsuhiko; Watanabe, Takanobu; Hoshino, Tadatsugu; Ohdomari, Iwao.

    In: Japanese Journal of Applied Physics, Part 1: Regular Papers and Short Notes and Review Papers, Vol. 44, No. 11, 09.11.2005, p. 8210-8215.

    Research output: Contribution to journalArticle

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