Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles

Amyloid fibril disaggregation has been observed recently upon incubation with lipid vesicles, challenging the view of fibrils as end states of the aggregation process in vivo. Here, we follow fibril disaggregation in the presence of lipid vesicles by means of molecular dynamics simulations, using simplified models of peptides and lipids. The simulation results show that disaggregation is driven by an entropy increase and yields soluble protofibrillar intermediates. These intermediates are different from themetastable oligomers observed during fibril formation, and their stability depends on the morphology of the parent fibril. SECTION Biophysical Chemistry A variety of proteins assemble into cross β-sheet structures (amyloid fibrils),mostly underdisease-relatedor nonphysiological conditions. Lipid membranes are able to catalyze fibril formation for a variety of peptides. Concomitantly, fibril growth on the membrane surface can damage the lipid bilayer. For example, leakage from lipid vesicles is observed during islet amyloid polypeptide fibril aggregation but not when the vesicles are incubated with preformed fibrils, indicating that the growth of fibrils on the membrane is harmful to the cells, unlike the fibrils themselves, which are considered harmless. Recently, this view has been questioned by a study in which soluble toxic oligomeric species were observed upon Aβ42 fibril degradation induced by lipid vesicles. Experimental characterization of forward (on-pathway) or backward oligomers is challenging due to their transient nature and to the mixture of monomeric, oligomeric, and fibrillar species that may be present at the same time. It is possible to conduct single-molecule experiments but not single-oligomer or single-fibril experiments. This gap can be filled in by molecular dynamics simulations. Simplified models of peptides are particularly useful for this aim because atomistic models are typically limited to time scales of 0.1-1 μs, which is many orders of magnitude shorter than the aggregation process. For this reason, we have developed a phenomenological two-state model of amphipathic aggregation-prone peptides to study amyloid aggregation. In simulations of the simplified peptides and a simple model of vesicle-forming lipids, it was observed that differences in the kinetics of fibril formation originate from different aggregation propensities of the peptides, a finding that has been confirmed by experiments afterward. Here, we follow fibril disaggregation in the presence of a lipid vesicle by means of molecular dynamics simulations, using phenomenological models of peptides and lipids. Our aim is to study fibril degradation due to interactions with lipid vesicles. We assume that the ability of lipid vesicles (particularly those made of brain lipid extract) to induce fibril degradation is mainly due to relative attraction between the peptides and the lipids. This assumption is based on experimental evidence that GM1-containing lipid vesicles slow down or prevent the formation of R-synuclein fibrils. GM1 vesicles strongly bind amyloidogenic peptides such as Rsynuclein and have also led to fibril disaggregation. While it is not possible in vitro to produce vesicles made only of GM1 (or to separate out the effects of specific lipids from vesicles prepared from a mixture of lipids extracted from the brain), the explicit treatment of individual intermolecular interactions in the simulations allows one tomodify only the relative strength of peptide/lipid interactions without affecting the internal energy landscape of the peptides or the lipids. Details about the peptide and lipid models are given in the Methods section and in refs 8 and 9. Briefly, the simplified peptide has a single degree of freedom with two energy minima corresponding to amyloid-competent and amyloid-protected states, and the peptides can fibrillate only in the former conformation. It is important to mention that our simple model of an amphipathic aggregation-prone peptide was developed to reflect the phenomenology of fibril formation experiments and is not meant to be compared to any particular (poly)peptide sequence. As an example, while the Received Date: November 27, 2009 Accepted Date: December 16, 2009