Conformational transitions of cyclic D,L-peptides

Hajime Okamoto, Tetsuo Yamada, Shuichiro Kihara, Kazumasa Takechi, Hiroyuki Takagi, Kyozaburo Takeda

    Research output: Contribution to journalArticle

    7 Citations (Scopus)

    Abstract

    Conformational transitions of cyclic D,L-hexapeptides have been studied by first-principles calculations. Geometry optimizations for 20 types of homoresidue cyclic D,L-hexapeptide revealed that the cyclic peptides have two types of energetically stable backbone (extended (E) and bound (B) types); and for each type, the amino acid side chains have two orientations (equatorial and axial). Among the four types of isomer [E-type equatorial (Eeq), B-type equatorial (Beq), E-type axial (Eax), and B-type axial (Bax)], Bax is the energetically most preferred by most of the 20 encoded amino acid residues, whereas Eax is the least preferred. A search for transition states indicated that six types of conformational transition are possible between the isomers of the cyclic peptide, i.e., the backbone-backbone conversions (Eeq-Beq and E ax-Bax transitions), the side chain-side chain conversions (Eeq-Eax and Beq-Bax transitions), and the simultaneous conversions of the backbone and the side-chain orientation (Eeq-Bax and Eax-Beq transitions). All the six transitions proceed with the breaking of the high molecular symmetry (S6) and go through the triangular (C3) intermediate structure with either equatorial or axial side-chain orientation.

    Original languageEnglish
    Pages (from-to)962-973
    Number of pages12
    JournalJournal of Computational Chemistry
    Volume30
    Issue number6
    DOIs
    Publication statusPublished - 2009 Apr 30

    Fingerprint

    Cyclic Peptides
    Peptides
    Isomers
    Amino acids
    Backbone
    Amino Acids
    Geometry
    Transition State
    First-principles Calculation
    peptide L
    Triangular
    Symmetry
    Optimization

    Keywords

    • Ab initio
    • Axial and equatorial
    • Cyclic peptide
    • Isomer
    • Transformation

    ASJC Scopus subject areas

    • Chemistry(all)
    • Computational Mathematics

    Cite this

    Okamoto, H., Yamada, T., Kihara, S., Takechi, K., Takagi, H., & Takeda, K. (2009). Conformational transitions of cyclic D,L-peptides. Journal of Computational Chemistry, 30(6), 962-973. https://doi.org/10.1002/jcc.21110

    Conformational transitions of cyclic D,L-peptides. / Okamoto, Hajime; Yamada, Tetsuo; Kihara, Shuichiro; Takechi, Kazumasa; Takagi, Hiroyuki; Takeda, Kyozaburo.

    In: Journal of Computational Chemistry, Vol. 30, No. 6, 30.04.2009, p. 962-973.

    Research output: Contribution to journalArticle

    Okamoto, H, Yamada, T, Kihara, S, Takechi, K, Takagi, H & Takeda, K 2009, 'Conformational transitions of cyclic D,L-peptides', Journal of Computational Chemistry, vol. 30, no. 6, pp. 962-973. https://doi.org/10.1002/jcc.21110
    Okamoto, Hajime ; Yamada, Tetsuo ; Kihara, Shuichiro ; Takechi, Kazumasa ; Takagi, Hiroyuki ; Takeda, Kyozaburo. / Conformational transitions of cyclic D,L-peptides. In: Journal of Computational Chemistry. 2009 ; Vol. 30, No. 6. pp. 962-973.
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