Amyloid-like Fibrils from a Domain-swapping Protein Feature a Parallel, in-Register Conformation without Native-like Interactions

Abstract

The formation of amyloid-like fibrils is characteristic of various diseases, but the underlying mechanism and the factors that determine whether, when, and how proteins form amyloid, remain uncertain. Certain mechanisms have been proposed based on the three-dimensional or runaway domain swapping, inspired by the fact that some proteins show an apparent correlation between the ability to form domain-swapped dimers and a tendency to form fibrillar aggregates. Intramolecular ␤-sheet contacts present in the monomeric state could constitute intermolecular ␤-sheets in the dimeric and fibrillar states. One example is an amyloid-forming mutant of the immunoglobulin binding domain B1 of streptococcal protein G, which in its native conformation consists of a four-stranded ␤-sheet and one ␣-helix. Under native conditions this mutant adopts a domainswapped dimer, and it also forms amyloid-like fibrils, seemingly in correlation to its domain-swapping ability. We employ magic angle spinning solid-state NMR and other methods to examine key structural features of these fibrils. Our results reveal a highly rigid fibril structure that lacks mobile domains and indicate a parallel in-register ␤-sheet structure and a general loss of native conformation within the mature fibrils. This observation contrasts with predictions that native structure, and in particular intermolecular ␤-strand interactions seen in the dimeric state, may be preserved in "domain-swapping" fibrils. We discuss these observations in light of recent work on related amyloidforming proteins that have been argued to follow similar mechanisms and how this may have implications for the role of domain-swapping propensities for amyloid formation.Amyloid fibril formation is characteristic of a variety of human disorders, including Huntington and Alzheimer diseases (1, 2). In amyloid-related diseases, one or more proteins are found in fibrillar aggregates, in a non-native, highly ␤-sheetrich conformation. Depending on the disease context, the propensity for amyloid formation may be traced to mutations and cleavage events, combined with poorly understood external triggers. Many proteins can also be made to form amyloid fibrils in vitro. Intriguingly, there are many accounts of proteins that form amyloid-like fibrils that are not associated with pathologies (2). Whether disease-related or not, amyloid fibrils share key biochemical and biophysical characteristics, suggesting common structural features. Understanding the fibril formation pathway is of interest not only as there may be a correlation between disease onset and protein aggregation, but also because transient oligomeric precursors may act as toxic species. However, a lack of high resolution structures of most fibrils and their precursors limits our knowledge of the mechanism of formation.One seemingly common structural motif for amyloid fibrils is an in-register parallel (IP) 3 assembly into pleated ␤-sheets, stabilized by backbone-to-backbone hydrogen bonding, combined with favorable side-chain interactions (e....

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