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Cyclic retro-inverso dipeptides with two aromatic side chains. II. Conformational analysis.

T Yamazaki1, K Nunami, M Goodman

  • 1Department of Chemistry, University of California, San Diego, La Jolla 92093-0343.

Biopolymers
|November 1, 1991
PubMed
Summary

Conformational studies of cyclic retro-inverso and parent dipeptides reveal distinct backbone preferences in trans isomers. These findings aid in refining force constants for aromatic peptide models.

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Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Organic Chemistry

Background:

  • Understanding peptide conformation is crucial for drug design and biomaterial development.
  • Cyclic peptides and their retro-inverso counterparts offer unique structural scaffolds.
  • Aromatic side chains significantly influence peptide folding and interactions.

Purpose of the Study:

  • To elucidate the conformational preferences of cis and trans cyclic retro-inverso and parent dipeptides.
  • To investigate the influence of backbone structure on side chain orientation.
  • To estimate conformational energies of specific bonds within retro-inverso dipeptides.

Main Methods:

  • 1H-NMR spectroscopy was employed to study molecular conformations.
  • Semiempirical energy calculations provided theoretical insights into stable conformers.

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  • Temperature-dependent NMR coupling constants were used to estimate bond energies.

    • Main Results:

    • Both cis and trans dipeptides exhibit 'face-to-face' or 'sandwich' arrangements of aromatic side chains.
    • Trans cyclic retro-inverso dipeptides adopt a single boat conformation, unlike parent dipeptides which show two.
    • Conformational energies for malonyl and gem-diamino residues were determined as 1.1 and 1.8 kcal/mol.

    Conclusions:

    • Distinct backbone conformational preferences exist between cyclic retro-inverso and parent dipeptides.
    • The estimated conformational energies accurately predict side chain distributions in parent dipeptides.
    • These findings are valuable for refining force fields used in modeling aromatic peptides.