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Related Experiment Videos

Structure-based engineering of internal cavities in coiled-coil peptides.

Maneesh K Yadav1, James E Redman, Luke J Leman

  • 1Department of Chemistry, The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Biochemistry
|July 13, 2005
PubMed
Summary

Researchers engineered internal cavities in peptides by altering amino acids. These designed cavities, characterized structurally, demonstrate potential for creating artificial enzymes and receptors.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Protein Engineering

Background:

  • Molecular cavities are crucial for biological interactions like enzyme-substrate binding.
  • Structural characterization of engineered cavities in peptides is limited.
  • Designing artificial catalysts and receptors requires understanding cavity formation.

Purpose of the Study:

  • To systematically investigate the structural consequences of single amino acid substitutions in peptide hydrophobic cores.
  • To characterize the formation and properties of internal cavities within designed peptides.
  • To explore the potential of these engineered cavities for molecular recognition.

Main Methods:

  • Synthesis of GCN4-based coiled-coil peptides with specific amino acid substitutions (glycine, serine, alanine, threonine) at core positions.

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  • Solution-phase techniques and crystallographic methods for structural analysis.
  • Investigation of peptide self-assembly into tetrameric structures and cavity formation.

    • Main Results:

    • All synthesized peptides formed stable tetramers with internal cavities ranging from 80 to 370 A(3).
    • Identical core substitutions yielded cavities of varying shapes and volumes depending on peptide configuration (parallel vs. antiparallel).
    • Two peptides (L9G and L9A) demonstrated binding of iodobenzene within their cavities, causing local conformational changes without disrupting overall structure.

    Conclusions:

    • Single amino acid substitutions effectively engineer diverse internal cavities in coiled-coil peptides.
    • Peptide configuration significantly influences cavity dimensions, highlighting design flexibility.
    • Engineered peptide cavities can bind small molecules, offering a foundation for de novo protein design and artificial receptor development.