Frustrated peptide chains at the fibril tip control the kinetics of growth of amyloid-β fibrils

Abstract

Amyloid fibrillization is an exceedingly complex process in which incoming peptide chains bind to the fibril while concertedly folding. The coupling between folding and binding is not fully understood. We explore the molecular pathways of association of Aβ40 monomers to fibril tips by combining time-resolved in situ scanning probe microscopy with molecular modeling. The comparison between experimental and simulation results shows that a complex supported by nonnative contacts is present in the equilibrium structure of the fibril tip and impedes fibril growth in a supersaturated solution. The unraveling of this frustrated state determines the rate of fibril growth. The kinetics of growth of freshly cut fibrils, in which the bulk fibril structure persists at the tip, complemented by molecular simulations, indicate that this frustrated complex comprises three or four monomers in nonnative conformations and likely is contained on the top of a single stack of peptide chains in the fibril structure. This pathway of fibril growth strongly deviates from the common view that the conformational transformation of each captured peptide chain is templated by the previously arrived peptide. The insights into the ensemble structure of the frustrated complex may guide the search for suppressors of Aβ fibrillization. The uncovered dynamics of coupled structuring and assembly during fibril growth are more complex than during the folding of most globular proteins, as they involve the collective motions of several peptide chains that are not guided by a funneled energy landscape.

Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies

“…Both CsgA and FapC show a log-linear relationship between elongation rate constants and [urea] between 0 and 8 M urea [63]. This rules out detectable intermediates during FuBA elongation, in contrast to Aβ1-40, which was recently proposed to go through a "frustrated" complex intermediate [82]. This is manifested as in increase in the elongation rate of Aβ up to 1.5 M urea [82], after which there is a decrease in the elongation rate, as described by other groups for both Aβ1-40 and Aβ1-42 [79,80].…”

“…This rules out detectable intermediates during FuBA elongation, in contrast to Aβ1-40, which was recently proposed to go through a "frustrated" complex intermediate [82]. This is manifested as in increase in the elongation rate of Aβ up to 1.5 M urea [82], after which there is a decrease in the elongation rate, as described by other groups for both Aβ1-40 and Aβ1-42 [79,80]. For globular proteins, an increase in folding rate with [denaturant] at low [denaturant] is evidence of an off-pathway species which has to unfold back to the denatured state for folding to proceed [83,84].…”

Exploring the Interplay between Disordered and Ordered Oligomer Channels on the Aggregation Energy Landscapes of α-Synuclein

“…In addition, however, we find another species with many interchain parallel hydrogen bonds. In this class, the number of interchain hydrogen bonds is more than for the disordered species but is fewer than for the fully ordered prefibrillar species, which are also found in Aβ aggregation . These species, which we call prefibrillar oligomers with disordered tips, are dominated by fibril-like β sheet chains with the addition of a few β hairpin chains at the ends.…”

“…In this class, the number of interchain hydrogen bonds is more than for the disordered species but is fewer than for the fully ordered prefibrillar species, which are also found in Aβ aggregation. 36 These species, which we call prefibrillar oligomers with disordered tips, are dominated by fibril-like β sheet chains with the addition of a few β hairpin chains at the ends. The existence of two kinds of species, the fully ordered prefibrillar oligomers and the prefibrillar oligomers with disordered tips, agrees with FRET experiments which suggest there are two classes of species when the oligomer size is larger than 5.…”

Elongation of Fibrils Formed by a Tau Fragment is Inhibited by a Transient Dimeric Intermediate

“…This would lead to inhibition of the elongation of the former complex but not of the latter complex (Figure S9). Interestingly, a previous study suggested that in the case of fibrils made of two protofilaments, the probability of monomer binding to fibril ends by non-native interactions, leading to retardation of fibril growth, would be high.…”