Molecular dynamical approach to the conformational transition in peptide nanorings and nanotubes

Masato Teranishi, Hajime Okamoto, Kyozaburo Takeda, Ken Ichi Nomura, Aiichiro Nakano, Rajiv K. Kalia, Priya Vashishta, Fuyuki Shimojo

    Research output: Contribution to journalArticle

    11 Citations (Scopus)

    Abstract

    We study the conformational transition in D, L-peptide nanorings (PNRs) and nanotubes (PNTs) computationally based on the total energy calculation. Ab initio energy calculation has been carried out to investigate the static states of PNRs, whereas the molecular dynamics (MD) calculation has been employed to examine PNRs' dynamical states. We, then, discuss the time-dependent (TD) feature via the transition process from E-type to B-type and vice versa. The conformational transition occurs easily from E-type equatorial (Eeq) to B-type axial (Bax) but is unreversible for the opposite direction because of a larger activation energy. The TD tracing of the two dihedral angles in the individual amino acid residues reveals that the conformational change propagates along the peptide skeleton ring nearly at the sound velocity. We further expand our study to the tubular forms and reveal that the PNT has an ability to produce the two kinds of homogeneous tubes, being composed of E rings (E-tube) and of B rings (B-tube), and also that these two PNRs should be mixed to produce a binary alloyed PNT.

    Original languageEnglish
    Pages (from-to)1473-1484
    Number of pages12
    JournalJournal of Physical Chemistry B
    Volume113
    Issue number5
    DOIs
    Publication statusPublished - 2009 Feb 5

    Fingerprint

    Peptide Nanotubes
    Nanorings
    Nanotubes
    Peptides
    peptides
    nanotubes
    tubes
    rings
    Acoustic wave velocity
    Dihedral angle
    Molecular dynamics
    tracing
    acoustic velocity
    musculoskeletal system
    Activation energy
    amino acids
    dihedral angle
    Amino acids
    Amino Acids
    molecular dynamics

    ASJC Scopus subject areas

    • Physical and Theoretical Chemistry
    • Materials Chemistry
    • Surfaces, Coatings and Films

    Cite this

    Teranishi, M., Okamoto, H., Takeda, K., Nomura, K. I., Nakano, A., Kalia, R. K., ... Shimojo, F. (2009). Molecular dynamical approach to the conformational transition in peptide nanorings and nanotubes. Journal of Physical Chemistry B, 113(5), 1473-1484. https://doi.org/10.1021/jp8067975

    Molecular dynamical approach to the conformational transition in peptide nanorings and nanotubes. / Teranishi, Masato; Okamoto, Hajime; Takeda, Kyozaburo; Nomura, Ken Ichi; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Shimojo, Fuyuki.

    In: Journal of Physical Chemistry B, Vol. 113, No. 5, 05.02.2009, p. 1473-1484.

    Research output: Contribution to journalArticle

    Teranishi, M, Okamoto, H, Takeda, K, Nomura, KI, Nakano, A, Kalia, RK, Vashishta, P & Shimojo, F 2009, 'Molecular dynamical approach to the conformational transition in peptide nanorings and nanotubes', Journal of Physical Chemistry B, vol. 113, no. 5, pp. 1473-1484. https://doi.org/10.1021/jp8067975
    Teranishi, Masato ; Okamoto, Hajime ; Takeda, Kyozaburo ; Nomura, Ken Ichi ; Nakano, Aiichiro ; Kalia, Rajiv K. ; Vashishta, Priya ; Shimojo, Fuyuki. / Molecular dynamical approach to the conformational transition in peptide nanorings and nanotubes. In: Journal of Physical Chemistry B. 2009 ; Vol. 113, No. 5. pp. 1473-1484.
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