Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence

Abstract

The small amyloid-forming GNNQQNY fragment of the prion sequence has been the subject of extensive experimental and numerical studies over the last few years. Using unbiased molecular dynamics with the OPEP coarse-grained potential, we focus here on the onset of aggregation in a 20-mer system. With a total of 16.9 of simulations at 280 K and 300 K, we show that the GNNQQNY aggregation follows the classical nucleation theory (CNT) in that the number of monomers in the aggregate is a very reliable descriptor of aggregation. We find that the critical nucleus size in this finite-size system is between 4 and 5 monomers at 280 K and 5 and 6 at 300 K, in overall agreement with experiment. The kinetics of growth cannot be fully accounted for by the CNT, however. For example, we observe considerable rearrangements after the nucleus is formed, as the system attempts to optimize its organization. We also clearly identify two large families of structures that are selected at the onset of aggregation demonstrating the presence of well-defined polymorphism, a signature of amyloid growth, already in the 20-mer aggregate.

Computational Studies of Protein Aggregation: Methods and Applications

“…The authors predicted a high degree of polymorphism of the sequence. Using conventional molecular dynamics simulations, they also analyzed the oligomerization kinetics of the same sequence (116). They found kinetics mostly consistent with classical nucleation theory, with a critical nucleus of four to five monomers.…”

Concluding the Amyloid Formation Pathway of a Coiled‐Coil‐Based Peptide from the Size of the Critical Nucleus

“…Thus, nucleated growth is often characterized by an apparent lag phase followed by rapid fibril growth. [33][34][35][36][37][38][39][40] A key step in the nucleation process, however, is the formation of oligomeric intermediate species, which are normally soluble and sometimes structurally unstable or metastable. These can include, for instance, partial unfolding or refolding, oligomerization, conformational conversion, elongation, condensation, and fragmentation.…”

“…A nucleus consisting of oligomeric aggregates can also be formed by native or native-like structures, and the conversion to amyloids subsequently takes place within the aggregates. [36][37][38] Here we calculated the nucleus size of a model peptide that has been previously established and well characterized in our group, [46][47][48][49][50][51][52][53] VW18, by applying the nucleated growth polymerization theory to experimental data. A wide range of experimental strategies is currently being developed to detect the actual nucleus size.…”

“…[32,33] Following the variety of kinetic behaviors depending on the protein and the experimental conditions, a number of models describing aggregation have been proposed. [33][34][35][36][37][38][39][40] A key step in the nucleation process, however, is the formation of oligomeric intermediate species, which are normally soluble and sometimes structurally unstable or metastable. [6,30,[41][42][43] Nucleation is mostly completed by the structural conversion of these small intermediate species into small prefibrillar structures that act as templates triggering the rapid fibril growth.…”

“…[34,35,40] Other approaches use theoretical methods such as molecular dynamics simulations or model based calculations to resolve the aggregation pathway. [36][37][38] Here we calculated the nucleus size of a model peptide that has been previously established and well characterized in our group, [46][47][48][49][50][51][52][53] VW18, by applying the nucleated growth polymerization theory to experimental data. [22,23,36,54] This approach requires monitoring amyloid formation rates over a wide span of peptide concentrations, as well as determining the critical concentration for amyloid formation, c crit .…”