Interactions Contributing to the Formation of a β-Hairpin-like Structure in a Small Peptide

Abstract

A 12 amino acid peptide, model BB, was designed to adopt a beta-hairpin tertiary structure in water that might be stabilized by a variety of local, nonlocal, polar, and nonpolar interactions. The conformational properties of model BB with and without an intramolecular disulfide bond (BB-O and BB-R, respectively) were characterized by NMR and CD spectroscopy. The set of observed short- and medium-range nOes were consistent with the formation of stable beta-hairpin-like structures by both BB-R and BB-O. BB-O adopts two distinct conformations that differ from each other in the designed reverse turn segment. A reasonably well-defined set of structures was obtained by using restraints from the NMR data in distance geometry calculations. None of the beta-hairpin-like structures contain a beta-sheet hydrogen bonding network. The distinctive feature of intrastrand and cross-strand pairing of threonine residues observed in all of the calculated structures suggests that hydrophobic interactions between the gamma-methyl groups of threonine residues may be the structure-determining interaction in model BB. The implications of these results for the formation of beta-sheets during protein folding, the aggregation of peptides as beta-sheets, and the de novo design of independently folding beta-hairpin-like peptides are considered.

Prediction of local structure in proteins using a library of sequence-structure motifs

“…The transposition of just two residues (DG3GD) causes the change from a type-I hairpin (below) to a diverging type-II turn. There is experimental evidence for a structure resembling this motif in a short peptide whose sequence matches this pattern (Sieber & Moe, 1996).…”

“…Experimental evidence for this comes from NMR studies of isolated peptides. For the most part, peptides of 30 residues or less are found not to have a well-de®ned structure in water (Itzhaki et al, 1995;Yang et al, 1995), but many of the notable exceptions correspond to I-sites motifs, including the Schellman cap (Viguera & Serrano, 1995), the N-capping box , the serine b-hairpin (Blanco et al, 1994), the type-I b-hairpin (de Alba et al, 1996;Ilyina et al, 1994;Searle et al, 1995), and the diverging type-II turn (Sieber & Moe, 1996). In each case, a predominant solution structure was found that closely resembled the paradigm structure of the I-sites cluster that best matched its sequence.…”

Equilibrium folding intermediates of a greek key β-barrel protein

“…In the EF b-hairpin, backbone NH groups of residues Lys49, Ile51, Gln54, Gly57, Ala59 and Val65 do not show exchange, evidencing a single, stable conformation. Previous demonstrations that small peptides can form stable b-hairpins in aqueous solution (Blanco et al, 1994;Searle et al, 1995;Sieber & Moe, 1996) provide indirect evidence that the EF b-hairpin serves as a folding nucleus. The EF b-hairpin is one of four so-called folded hairpins which are a prominent feature of the protein S and bg-crystallin structures (Bagby et al, 1994a;Lapatto et al, 1991).…”

β‒hairpin polypeptides by design and selection

“…2. Hydrophobic residues, especially those with aromatic rings, are found to be stabilizing, with tryptophan being the best (the importance of cross-strand hydrophobic interactions has been hinted at in previous studies of β-hairpins [3,31,39,47]). The trend observed in Fig.…”

“…This was done in the context of a 10-residue peptide with cysteine residues at position 1 and 10, threonine residues at position 2 and 9 (this amino acid tends to favor an extended backbone [35,51]), and a Glu-Gly-AsnLys sequence for residues 4-7 as it should have a moderate tendency to form a type II reverse turn [24]. Position 8 was initially chosen to be leucine, and naturally-occurring amino acids were substituted at [41][42][43][44][45][46][47][48][49][50][51][52][53][54][55][56]; ∆∆G estimated assuming additivity of data for trpzip4, 5 and 6. b Spaces separate strand from turn residues; substitutions in the gb1 C-terminal peptide are indicated bold and underlined. position 3 (the X3L8-series), with the aim of identifying the residue that most stabilized the β-hairpin structure [10].…”