Analysis of the conformational profile of trishomocubane amino acid dipeptide

Krishna Bisetty, Penny Govender, Hendrik G. Kruger

Research output: Contribution to journalArticlepeer-review

19 Citations (Scopus)

Abstract

4-Amino-(D3)-trishomocubane-4-carboxylic acid is a constrained α-amino acid residue that exhibits promising conformational characteristics, i.e., helical and β-turns. As part of the development of conformational guidelines for the design of peptides and protein surrogates, the conformational energy calculations on trishomocubane using molecular mechanics and ab initia methods are presented. The Cα carbon of trishomocubane forms part of the cyclic structure, and consequently a peptidic environment was simulated with an acetyl group on its N-terminus and a methylamide group on its C-terminus. Ramachandran maps computed at the molecular mechanics level using the standard AMBER (parm94) force field libraries compared reasonably well with the corresponding maps computed at the Hartree Fock level, using the 6-31G* basis set. Trishomocubane peptide (Ac-Tris-NHMe) is characterized by four low energy conformers corresponding to the C7ax, C7eq, 310, and αL helical structures.

Original languageEnglish
Pages (from-to)339-349
Number of pages11
JournalBiopolymers
Volume81
Issue number5
DOIs
Publication statusPublished - 5 Apr 2006

Keywords

  • AMBER (parm94)
  • Ab initio
  • Cage dipeptide
  • Conformational study
  • Molecular mechanics
  • Trishomocubane
  • Unnatural amino acids

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

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