The aggregation of proteins into stable, well-ordered structures known as amyloid fibrils has been associated with many neurodegenerative diseases. Amyloid fibrils are long straight, and un-branched structures containing several proto-filaments, each of which exhibits “cross beta structure,” – ribbon-like layers of large beta sheets whose strands run perpendicular to the fibril axis. It has been suggested in the literature that the pathway to fibril formation has the following steps: unfolded monomers associate into transient unstable oligomers, the oligomers undergo a rearrangement into the cross-β structure and form into proto-filaments, these proto-filaments then associate and grow into fully formed fibrils. Recent experimental studies have determined that the unstable intermediate structures are toxic to cells and that their presence may play a key role in the pathogenesis of the amyloid diseases. Many efforts have been made to determine the structure of intermediate oligomer aggregates that form during the fibrillization process. The goal of this work is to provide details about the structure and formation kinetics of the unstable oligomers that appear in the fibril formation pathway.

The specific aims of this work are to determine the steps in the fibril formation pathway and how the kinetics of fibrillization changes with variations in temperature and concentration. The method used is the application of discontinuous molecular dynamics to large systems of peptides represented with an intermediate resolution model, PRIME, that was previously developed in our group. Three different peptide sequences are simulated: polyalanine (KA₁₄K), Aβ_17-40, and Aβ_17-42; the latter two are truncated sequences of the Alzheimer's peptide. We simulate the spontaneous assembly of these peptide chains from a random initial configuration of random coils.

We investigate aggregation kinetics and oligomer formation of a system of 192 polyalanine (KA₁₄K) chains over a variety of temperatures and concentrations. The fibril formation pathway has the following steps: free monomers associate into small amorphous aggregates, those small amorphous aggregates grow, the amorphous aggregates rearrange into β-sheets, and finally the β-sheets stack into small fibrillar structures. The rate of fibril formation increases as concentration increases and temperature decreases; this faster fibril formation is the combination of several effects, including increased amorphous aggregate formation from free monomers, increased amorphous aggregate rearrangement into β-sheets, and increased stacking into small fibrils. There is a competition between enthalpy and entropy that determine the behavior of the final structure in the system. At low temperature, enthalpy is dominant and the system produces multiple large fibrils, while at high temperature entropy is dominant and the system produces one or no large fibrils. As temperature increases and concentration decreases the intermediate structures that form, such as β-sheets and large independent amorphous aggregates, are more stabilized which leads to slower fibril formation and fewer chains in the large final fibrillar structure.

We study the formation of β-sheets and small fibrillar structures for both Aβ_17-40 and Aβ_17-42 to determine the difference between the two sequences in aggregation kinetics and oligomer structure as a function of temperature. We observe that at low temperatures, both Aβ_17-40 and Aβ_17-42 form large amorphous aggregates with a small amount of β-sheet character, at intermediate temperatures the peptides form a mixture of β-sheets and fibrils that are surrounded by amorphous aggregates, and at high temperatures the peptides form small amorphous aggregates or remain isolated as free monomers. Aβ _17-42 forms fibrils over a larger temperature range than Aβ _17-40. The structure of the β-sheets changes as temperature increases through the range conducive to fibril formation. Aβ_17-42 goes through the transition from predominantly intra-strand hydrogen bonds to predominantly inter-strand hydrogen bonds in the β-sheet structure at a higher temperature than Aβ_17-40.