A critical assessment of the role of helical intermediates in amyloid formation by natively unfolded proteins and polypeptides

Abstract

Amyloidogenic proteins and polypeptides can be divided into two structural classes, namely those which are flexible and are intrinsically disordered in their unaggregated state and those which form a compact globular structure with a well-defined tertiary fold in their normally soluble state. This review article is focused on amyloid formation by natively disordered polypeptides. Important examples of this class include islet amyloid polypeptide (IAPP, amylin), pro-IAPP processing intermediates, alpha-synuclein, the Abeta peptide, atrial natriuretic factor, calcitonin, pro-calcitonin, the medin polypeptide, as well as a range of de novo designed peptides. Amyloid formation is a complex process consisting of a lag phase during which no detectable fibril material is formed, followed by a rapid growth phase that leads to amyloid fibrils. A critical analysis of the literature suggests that a subset of intrinsically disordered polypeptides populate a helical intermediate during the lag phase. In this scenario, early formation of multimeric species is promoted by helix-helix association involving one region of the polypeptide chain which leads to a high effective concentration of an amyloidogenic sequence located in a different region of the chain. Helical intermediates appear to be particularly important in membrane-catalyzed amyloid formation and have been implicated in glycosaminoglycan mediated amyloid formation as well. There is suggestive evidence that targeting helix-helix interactions can be a viable strategy to inhibit amyloid formation. The characterization of transient helical intermediates is challenging, but new methods are being developed that offer the prospect of providing residue-specific information in real time.

Fig. 1

A schematic diagram of how an α-helical intermediate might promote amyloid formation. α-Helices are depicted as cylinders, β-strands as zigzagged lines. Initial oligomerization is driven by the thermodynamic linkage between self-association and helix formation (step 1). This in turn generates a high local concentration of a region of the protein chain which has a high propensity to adopt β-structure. Propagation of β-structure leads to the formation of β-sheet-rich assemblies. The diagram is schematic and is not meant to imply a specific pathway of assembly. A tetramer is shown here for the purposes of illustration, but a range of oligomeric species could be formed. The diagram implies a sequential zipping of the β-strands and unwinding of the helices, but this is simply meant to be illustrative and a diversity of pathways is likely.

Fig. 2

A schematic diagram of how a hypothetical inhibitor which combines a helix recognition motif with a β-sheet breaker could act as an inhibitor. The diagram is meant to represent a mutant of an amyloidogenic peptide in which the mutation (depicted as an X) is located in a region outside of the helix recognition motif, but within a region critical for conversion to β-structure. Some IAPP point mutants may act via this mechanism.