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

Keywords

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

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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  • 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