Interplay among side chain sequence, backbone composition, and residue rigidification in polypeptide folding and assembly

Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9151-6. doi: 10.1073/pnas.0801135105. Epub 2008 Jun 27.

Abstract

The extent to which polypeptide conformation depends on side-chain composition and sequence has been widely studied, but less is known about the importance of maintaining an alpha-amino acid backbone. Here, we examine a series of peptides with backbones that feature different repeating patterns of alpha- and beta-amino acid residues but an invariant side-chain sequence. In the pure alpha-backbone, this sequence corresponds to the previously studied peptide GCN4-pLI, which forms a very stable four-helix bundle quaternary structure. Physical characterization in solution and crystallographic structure determination show that a variety of alpha/beta-peptide backbones can adopt sequence-encoded quaternary structures similar to that of the alpha prototype. There is a loss in helix bundle stability upon beta-residue incorporation; however, stability of the quaternary structure is not a simple function of beta-residue content. We find that cyclically constrained beta-amino acid residues can stabilize the folds of alpha/beta-peptide GCN4-pLI analogues and restore quaternary structure formation to backbones that are predominantly unfolded in the absence of cyclic residues. Our results show a surprising degree of plasticity in terms of the backbone compositions that can manifest the structural information encoded in a sequence of amino acid side chains. These findings offer a framework for the design of nonnatural oligomers that mimic the structural and functional properties of proteins.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Circular Dichroism
  • Crystallography, X-Ray
  • Cyclization
  • Molecular Sequence Data
  • Peptides / chemistry*
  • Peptides / metabolism*
  • Protein Folding*
  • Protein Structure, Secondary

Substances

  • Peptides

Associated data

  • PDB/3C3F
  • PDB/3C3G
  • PDB/3C3H