Mechanisms and rates of nucleation of amyloid fibrils

Abstract

The classical nucleation theory finds the rate of nucleation proportional to the monomer concentration raised to the power, which is the 'critical nucleaus size', n c . The implicit assumption, that amyloids nucleate in the same way, has been recently challenged by an alternative two-step mechanism, when the soluble monomers first form a metastable aggregate (micelle), and then undergo conversion into the conformation rich in β-strands that are able to form a stable growing nucleus for the protofilament. Here we put together the elements of extensive knowledge about aggregation and nucleation kinetics, using a specific case of Aβ 1−42 amyloidogenic peptide for illustration, to find theoretical expressions for the effective rate of amyloid nucleation. We find that at low monomer concentration in solution, and also at low interaction energy between two peptide conformations in the micelle, the nucleation occurs via the classical route. At higher monomer concentration, and a range of other interaction parameters between peptides, the two-step 'aggregation-conversion' mechanism of nucleation takes over. In this regime, the effective rate of the process can be interpreted as a power of monomer concentration in a certain range of parameters, however, the exponent is determined by a complicated interplay of interaction parameters and is not related to the minimum size of the growing nucleus (which we find to be ∼ 7-8 for Aβ 1−42 ).

Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide

“…The free energy barrier for oligomer conversion is lower at higher monomer concentrations, which explains the observation that the fraction of oligomers that dissociate without forming new fibrils is lower at higher monomer concentrations. The non-classical nucleation behaviour described here for Aβ42 fibril formation is analogous to the two-step nucleation processes observed in crystallisation, bio-mineralisation and sickle-cell haemoglobin 26,27,[34][35][36][37][38][39]. Moreover, we have established the absence, in our system, of detectable quantities of persistent off-pathway oligomers that cannot convert to fibrils over the timescale of aggregation, although such species may exist under different experimental conditions or for other, particularly larger, amyloidogenic proteins such as α-synuclein 40.…”

“…The non-classical nucleation behaviour described here for Aβ42 fibril formation is analogous to the two-step nucleation processes observed in crystallisation, bio-mineralisation and sickle-cell haemoglobin. 26,27,[34][35][36][37][38][39] Moreover, we have established the absence, in our system, of detectable quantities of persistent off-pathway oligomers that cannot convert to fibrils over the timescale of aggregation, although such species may exist under different experimental conditions or for other, particularly larger, amyloidogenic proteins such as α-synuclein. 40 More generally, our work could be extended to study oligomer dynamics in peptide mixtures; in the presence of additional inhibitors, 41 11 these experiments could inform upon the role of off-pathway oligomers in such systems.…”

Universality of filamentous aggregation phenomena

“…These species are likely micellar in nature, possess low β-sheet content, and are thus structurally distinct from mature fibrils, as observed both in experiments [34] and in computer simulations [30,[35][36][37]. The rate law employed in our model equation 1bis a coarse-grained description of these nonclassical nucleation processes, which can be justified from an explicit consideration of the free-energy landscape in aggregate size and structural space (see [37,38] for further details). This calculation shows that the exponents n c and n 2 , which represent the reaction orders of primary and secondary nucleation with respect to the free-monomer concentration, are not related to the overall physical size of the nucleating aggregates as in classical nucleation theory.…”

“…This calculation shows that the exponents n c and n 2 , which represent the reaction orders of primary and secondary nucleation with respect to the free-monomer concentration, are not related to the overall physical size of the nucleating aggregates as in classical nucleation theory. Instead, n c and n 2 are related to the portion of the nucleating aggregate that actively participates in the conformational conversion of oligomers to fibrils [37,38].…”

Slow Dissolution Kinetics of Model Peptide Fibrils

“…Based on these data, a kinetic model for the fibril formation process could be developed [ 15 ], taking into account both primary and secondary nucleation processes. The nucleation process may also involve disordered complexes [ 16 ] and well-defined oligomer states [ 15 , 17 ]. It has also recently been suggested that some molecular pathways may be intrinsically catalytic in their nature, such that they can display saturation effects [ 18 ].…”