Analysis of interactions between luciferase and si substrates using molecular dynamics simulations

Katsuhiko Nishiyama, Takanobu Watanabe, Tadatsugu Hoshino, Iwao Ohdomari

    Research output: Contribution to journalArticle

    5 Citations (Scopus)

    Abstract

    A series of molecular dynamics (MD) simulations have been performed to investigate the interactions between luciferase and Si substrates. The results show that luciferase adsorbs directly on the hydrophobic Si substrate, and via water molecules on the hydrophilic one. The adsorption-induced changes in conformation of luciferase are smaller on the hydrophilic Si substrate than on the hydrophobic one. The dynamic atom motions in luciferase are larger on the hydrophilic Si substrate than on the hydrophobic one. Inside the active site, the adsorption-induced changes in distances between the atoms forming hydrogen bonds to substrate luciferin are smaller on the hydrophilic Si substrate than the hydrophobic one. In order to prevent the denaturation of luciferase caused by immobilization, the solid surface should be hydrophilic. For higher thermostability, after immobilization, however, a hydrophobic surface is preferable since the dynamic atom motions in luciferase are smaller on a hydrophobic surface. The solid surface should be prepared delicately both from the viewpoint of preventing the denaturation caused by immobilization and improving the thermostability.

    Original languageEnglish
    Pages (from-to)1021-1025
    Number of pages5
    JournalJapanese Journal of Applied Physics, Part 1: Regular Papers and Short Notes and Review Papers
    Volume45
    Issue number2 A
    DOIs
    Publication statusPublished - 2006 Feb 8

    Fingerprint

    Molecular dynamics
    molecular dynamics
    Computer simulation
    Substrates
    immobilization
    Denaturation
    simulation
    biopolymer denaturation
    interactions
    solid surfaces
    Atoms
    thermal stability
    atoms
    Adsorption
    adsorption
    Conformations
    Hydrogen bonds
    hydrogen bonds
    Molecules
    water

    Keywords

    • Biomedical application
    • Luciferase
    • MD
    • Molecular dynamics simulations
    • Nanostructure
    • Protein chip
    • Si substrates

    ASJC Scopus subject areas

    • Physics and Astronomy (miscellaneous)

    Cite this

    Analysis of interactions between luciferase and si 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. 45, No. 2 A, 08.02.2006, p. 1021-1025.

    Research output: Contribution to journalArticle

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