Scrutinizing the squeezed exponential kinetics observed in the folding simulation of an off-lattice Go-like protein model

Hironori K. Nakamura, Masaki Sasai, Mitsunori Takano

    Research output: Contribution to journalArticle

    16 Citations (Scopus)

    Abstract

    We investigated whether the squeezed exponential kinetics, which was found in the previous Monte Carlo simulation of a lattice Go model for protein folding, can be observed as well in the molecular dynamics simulation (MD) of an off-lattice Go-like model. It was shown that the squeezed-exponential-type folding kinetics is indeed observed in the off-lattice Go-like model. Then, the effects of the native structure topology, the initial condition of the folding reaction, the employed observable to monitor folding reaction, and the time resolution of the kinetics data, on the observed squeezed exponential kinetics were investigated. The analysis of the time-resolution effect showed that the squeezed exponential kinetics can be attributed to the characteristics of the early stage of folding kinetics, suggesting that the squeezed exponential kinetics is most likely to be observed in experiment which focuses on the early stage of folding kinetics.

    Original languageEnglish
    Pages (from-to)259-267
    Number of pages9
    JournalChemical Physics
    Volume307
    Issue number2-3 SPEC.ISS.
    DOIs
    Publication statusPublished - 2004 Dec 27

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    folding
    proteins
    Kinetics
    kinetics
    Proteins
    simulation
    Protein folding
    Molecular dynamics
    topology
    Topology
    molecular dynamics
    Computer simulation
    Experiments

    ASJC Scopus subject areas

    • Physical and Theoretical Chemistry
    • Spectroscopy
    • Atomic and Molecular Physics, and Optics

    Cite this

    Scrutinizing the squeezed exponential kinetics observed in the folding simulation of an off-lattice Go-like protein model. / Nakamura, Hironori K.; Sasai, Masaki; Takano, Mitsunori.

    In: Chemical Physics, Vol. 307, No. 2-3 SPEC.ISS., 27.12.2004, p. 259-267.

    Research output: Contribution to journalArticle

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