Peptides with zip: small molecules for structure prediction

Abstract

Structural biologists have long been perplexed by how a protein's amino acid sequence determines its tertiary structure. To develop algorithms for structure predictions, researchers synthesize small model peptides and determine their conformations. Typically, however, these isolated peptides have limited stability relative to similar structural motifs within proteins. Stably folded peptides of less than 30 residues have been engineered previously by incorporating a conformationally restricted D-proline residue or a disulfide bond. Now, Cochran et al. 1xTryptophan zippers: stable, monomeric β-hairpins. Cochran, A.G. et al. Proc. Natl. Acad. Sci. USA. 2001; 98: 5578–5583Crossref | PubMed | Scopus (400)See all References1 have demonstrated a highly stable peptide motif that folds in the absence of metal ions, disulfide bonds, or unnatural amino acids. Because of the role of cross-strand tryptophan residues, they term this motif a tryptophan zipper (trpzip).Building on their previous studies of disulfide-cyclized peptides that form β-hairpins, the researchers designed short (12–16 residues) peptides containing four tryptophan residues in nonhydrogen-bonded positions. The tryptophans were arranged such that they formed two cross-strand pairs in a folded hairpin. Indeed, CD spectroscopy indicated that the water-soluble hairpins fold spontaneously in the absence of a covalent disulfide constraint. NMR structures showed that the indole rings of opposing tryptophans interdigitate on the peptide surface, making a β-hairpin significantly more stable than previously observed β-structures. Similar structures were observed for a variety of turn sequences and peptide lengths, suggesting that the trpzip is a general motif that depends primarily on proper spacing of the tryptophan residues.Flexible surface loops on proteins and bioactive peptides have been implicated in cellular recognition events, and might provide targets for novel therapeutics. However, given the marginal structural stability of most small peptides, large-scale screening for drug candidates has been limited. The authors have tipped their collective hand in pointing out potential trpzip sequences in V4 loops of the HIV glycoprotein gp120. This loop is unstructured in the gp120 crystal structure, but Cochran et al. 1xTryptophan zippers: stable, monomeric β-hairpins. Cochran, A.G. et al. Proc. Natl. Acad. Sci. USA. 2001; 98: 5578–5583Crossref | PubMed | Scopus (400)See all References1 synthesized one V4 peptide and confirmed the presence of a stable β-hairpin. The stabilizing influence of tryptophans in the trpzip motif was unexpected and points again to the challenge of predicting structure from sequence. This surprisingly stable structural scaffold will be a useful tool for protein modeling studies and drug discovery.