Increasing sequence length favors .alpha.-helix over 310-helix in alanine-based peptides: Evidence for a length-dependent structural transition

Abstract

Ala-based peptides form marginally stable helices at low temperature and are conventionally considered as mixtures of alpha-helix and random coil. However, recent work with doubly spin-labeled peptides suggests that short 16-residue sequences contain a significant fraction of 3(10)-helix near the N-terminus (positions 4-8). Using the same double-label strategy, we report on the helix geometry of the peptides Ac-(AAAAK)nA-NH2 with n = 3 and n = 4. The 16-mer (n = 3) is now examined at a region near the C-terminus, and there is evidence for 3(10)-helix here as well. The 21-mer (n = 4) is examined in three regions of the sequence. In dramatic contrast to the 16-mer, the 21-mer exhibits the signature of alpha-helix at the N-terminus and on through the middle of the peptide. The 21-mer C-terminus, however, adopts the 3(10)-helix geometry as is often found for C-termini in protein alpha-helices. These data indicate that the proportion of alpha-helix and 3(10)-helix in Ala-based peptides depends upon the sequence length.

Determination of the distance between two spin labels attached to a macromolecule.

“…To test the method, alanine-based a-helical peptides were synthesized (8,19,20). In 20 mol % trifluoroethanol, these are known to be a-helices.…”

“…[7] Thus, the average splitting (2B) for a given P(r), and subsequently the average separation of the two nitroxides, is obtained from: [8] and (r) = (Q.75(-)geI3/(2B)) * [9] The variance Sr of P(r) is also calculated from M(B):…”

“…One or two native residues are mutated to cysteines, which are then labeled with thiol-specific nitroxide spin labels. This technique can also be used to study local secondary structure (7,8). Nucleic acids also appear to be amenable to spin labeling (9).…”

UV Resonance Raman Investigation of a 310-Helical Peptide Reveals a Rough Energy Landscape

“…These studies have provided detailed microscopic knowledge of the folding energy landscape of these isolated motifs. Theoretical simulations have suggested that 3 10 -helices and/or type III -turns may serve as intermediates in the R-helix folding pathway (34)(35)(36)(37)(38)(39). The formation of kinetic intermediates such as -turn or 3 10 -helix lowers the entropic cost of nucleating the first helical residue, thus facilitating the helix folding transition (34,40,41).…”

“…Recent ESR (39,42) and NMR (43) work by Millhauser et al (41) suggests the presence of 3 10 -helix at the terminus of short alanine-based helical peptides. The authors proposed that 3 10 -helices are a relic of the folding process.…”