Simple polyglutamine (polyQ) peptides aggregate in vitro via a nucleated growth pathway directly yielding amyloid-like aggregates. We show here that the 17 amino acid flanking sequence (httNT) N-terminal to the polyQ in the toxic huntingtin exon1 fragment imparts onto this peptide a complex alternative aggregation mechanism. In isolation the httNT peptide is a compact coil that resists aggregation. When polyQ is fused to this sequence, it induces in httNT, in a repeat-length dependent fashion, a more extended conformation that greatly enhances its aggregation into globular oligomers with httNT cores and exposed polyQ. In a second step, a new, amyloid-like aggregate is formed with a core composed of both httNT and polyQ. The results indicate unprecedented complexity in how primary sequence controls aggregation within a substantially disordered peptide, and have implications for the molecular mechanism of Huntington's disease.

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Models of protein folding often hypothesize that the first step is local secondary structure formation. The assumption is that unfolded polypeptide chains possess an intrinsic propensity to form these local secondary structures. On the basis of this idea, it is tempting to model the local conformational properties of unfolded proteins using well-established residue secondary structure propensities, in particular, alpha-helix forming propensities. We have used spectroscopic methods to investigate the conformational behavior of a host-guest series of peptides designed to model unfolded alpha-helices. A suitable peptide model for unfolded alpha-helices was determined from studies of the length dependence of the conformational properties of alanine-based peptides. The chosen host peptide possessed a small, detectable, alpha-helix content. Substituting various representative guest residues into the central position of the host peptide at times changed the conformational behavior dramatically, and often in ways that could not be predicted from known alpha-helix forming propensities. The data presented can be used to rationalize some of these propensities. However, it is clear that secondary structure propensities cannot be used to predict the local conformational properties of unfolded proteins.

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