Insights into structures of peptide aggregation nuclei from concentration dependence of lag time

Abstract

Many peptides and proteins self-assemble into large fibrillar aggregates, reaching sizes of several micrometers. This process typically involves nucleation, formation of transient oligomeric species ranging from dimers to assemblies comprising hundreds of monomers. The roles of these heterogeneous oligomers in initiating fibril growth vary significantly, as only a subset converts into primary nuclei, the smallest assemblies capable of spontaneous elongation. Consequently, the initial stages of peptide aggregation remain a critical challenge in elucidating amyloid fibril formation. Here, we analyze the aggregation lag time as a function of initial peptide concentration, employing linear regression on a double logarithmic scale to derive the critical nucleus size from the slope. We compare potential shifts in kinetic regimes with critical concentrations associated with the assembly of larger oligomers. Although peptide length has no clear correlation with nucleus size, extended helical regions may promote the formation of larger nuclei, stabilizing preliminary oligomers and prolonging the lag phase. We quantified the contributions of higher-order oligomers as on- and off-pathway species across multiple peptides, identifying a common critical micelle concentration range. We prove that linear growth models can not capture the weak concentration dependence of lag times for several peptides. We demonstrate that the inclusion of capping and fragmentation mechanisms substantially improves the plausibility of the model. Knowledge of nucleus size facilitates molecular dynamics simulations to capture transitions to fibril-prone conformations. The insights advance our understanding of amyloid nucleation, identifying toxic aggregates in human neuroglial cells, and research on drug safety and biotechnological applications.