Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils

Abstract

Increasing evidence indicates that oligomeric protein assemblies may represent the molecular species responsible for cytotoxicity in a range of neurological disorders including Alzheimer and Parkinson diseases. We use all-atom computer simulations to reveal that the process of oligomerization can be divided into two steps. The first is characterised by a hydrophobic coalescence resulting in the formation of molten oligomers in which hydrophobic residues are sequestered away from the solvent. In the second step, the oligomers undergo a process of reorganisation driven by interchain hydrogen bonding interactions that induce the formation of β sheet rich assemblies in which hydrophobic groups can become exposed. Our results show that the process of aggregation into either ordered or amorphous species is largely determined by a competition between the hydrophobicity of the amino acid sequence and the tendency of polypeptide chains to form arrays of hydrogen bonds. We discuss how the increase in solvent-exposed hydrophobic surface resulting from such a competition offers an explanation for recent observations concerning the cytotoxicity of oligomeric species formed prior to mature amyloid fibrils.

Direct characterization of amyloidogenic oligomers by single-molecule fluorescence

“…This notion is supported by a previous study in which only amorphous aggregates comprising Ͼ20 molecules of a tandem repeat construct of PI3-SH3 (equal to Ͼ40 individual domains), were found to be efficient in promoting ordered fibril formation (20). Furthermore, a recent molecular simulation study has shown that for a small fragment from the ␤-amyloid peptide (A␤ 16 -22 ), the barrier for the conformational conversion of disordered oligomers into ␤-sheet-rich structures is lower for larger species (29,30). Taken together, these findings indicate that although a broad ensemble of oligomer sizes may populate the pathway for amyloid fibril formation, oligomers within a specific range of sizes are required for efficient conversion into more ordered species.…”

“…4B for a sample incubated under aggregation conditions for 72 h. A plausible cause of this enhancement in stability is an internal conformational reorganization of the oligomeric species populated during the reaction that leads to fibril formation. Interestingly, such a process has been predicted in computer simulations of the early stages of amyloid formation and attributed to the nucleation of the cross-␤ structure within species whose coalescence is initially driven by the rapid formation of less stable hydrophobic interactions (29).…”

Experimental characterization of disordered and ordered aggregates populated during the process of amyloid fibril formation

“…Several mechanisms have been proposed to explain amyloid fibril formation (24); among them, the nucleated conformational conversion (NCC) mechanism (25) is supported by a range of experimental and theoretical observations (26)(27)(28). In the NCC mechanism, a group of monomers initially present in solution coalesce to form amorphous oligomers.…”

“…3C), further reinforces the conclusion that a conformational change has occurred before their formation. This antibody is likely to recognize conformational characteristics of the intermediate species, perhaps because of the exposure of hydrophobic side chains (28,29) or the adoption of a different conformational form (30). The most protected residues in the O agg species are also the most protected ones in the F agg species, implying that these intermediates are likely to be species that progress to fibril formation.…”

Mechanism of amyloidogenesis: nucleation-dependent fibrillation versus double-concerted fibrillation

“…Hence, critical role of the oligomeric species isolated in the middle of fibrillation process should be acknowledged to evaluate the mechanism of amyloid fibril formation by acting as the seeds or the growing unit for the fibrillar assembly, in addition to their suggested pathological activity of causing cytotoxicity (104,105).…”