Supersaturation-limited and Unlimited Phase Transitions Compete to Produce the Pathway Complexity in Amyloid Fibrillation

Abstract

Background: Relationship between amyloid fibrils and amorphous aggregates has not yet been elucidated. Results: A competitive mechanism of amyloid fibrillation and amorphous aggregation reproduced the observed aggregation kinetics of ␤ 2 -microglobulin. Conclusion: Apparent complexities in amyloid fibrillation are explained assuming supersaturation-limited crystal-like amyloid fibrils and unlimited glass-like amorphous aggregates. Significance: Linkage of the kinetics of protein aggregation and a conformational phase diagram improves the understanding of protein aggregation.

Measurement of amyloid formation by turbidity assay—seeing through the cloud

“…Hall and coworkers explored the case where amyloid is more thermodynamically stable than the amorphous aggregate, but slower to initially form (Hall et al 2015). This study, along with work by Adachi et al (2015), highlighted a potential dependence of the time-scale of amyloid formation on the dissociation rate of the amorphous species.…”

“…The production of such amorphous aggregates has been observed in many amyloid-forming systems and often complicates simple interpretation of the reaction. Hall et al (2015) and Adachi et al (2015) have treated the case of amyloid growth in competition with amorphous aggregate using a kinetic rate scheme that treated the rate of growth and breakage of all species in an explicit fashion. Here we produce example simulations describing the competition between the amyloid and amorphous aggregate based on a fixed-seeded growth model (Naiki et al 1997).…”

“…To explore the effects of competing amorphous growth in extension to that performed previously (Adachi et al 2015; Hall et al 2015), we simulated three cases of competition between amorphous aggregate and amyloid using the consensus model presented in Table 2 (Fig. 13).…”

“…As such, our review differs from many others on the topic of amyloid biophysics (Hall and Edskes 2012; Kashchiev 2015; Ma and Nussinov 2006; Mezzenga and Fischer 2013; Sasahara and Goto 2013; So et al 2016; Tycko and Wickner 2013) by its restriction to matters directly related to achieving an understanding of the turbidimetric method. Towards this goal our examination will pay particular attention to recent articles concerned with ultra-microscope image analysis (Hall 2012; Usov and Mezzenga 2015), light scattering and turbidity development by protein aggregates (Garcia-Lopez and Garcia-Rubio 2008; Garcia-Lopez et al 2006; Hall et al 2016a) and simulation of the kinetics of amyloid (Ghosh et al 2010; Hall et al 2016b; Kaschiev 2015) and other aggregate types (Adachi et al 2015; Hall et al 2015). Although placing the focus of the review on a single type of assay procedure may seem like a retreat from the bigger questions, such as the relation between amyloid and disease (Hall and Edskes 2012; Walker and Jucker 2015), we contend that a thorough understanding of principles associated with the turbidimetric monitoring of amyloid growth will sharpen our collective ability to make informed judgements about the biological implications of results gained from in vitro protein aggregation assays.…”

What Can the Kinetics of Amyloid Fibril Formation Tell about Off-pathway Aggregation?

“…By expressing the driving force for protein aggregation as the thermodynamic supersaturation ϭ (C Ϫ C a * )/C a * (an approximation to the variation in chemical potential), the steady-state monomer concentration is expected to correspond to the amyloid solubility C ∞ ϭ C a * . At the same time that the CLM was being proposed, Yoshimura et al (33) urged the need to recognize amyloidogenicity as a property determined by the monomer concentration relative to solubility; since then, a wealth of new evidence has unanimously confirmed supersaturation as a major driving force for protein aggregation (6,11,34,35,36,37,38). Although this parallel with crystallization had been hinted at before (21,39), the common practice in literature models is to assume the monomer concentration alone as the driving force for phase transition (18,28,29,30,31), meaning that, for example, amyloid fibrils would continue to grow until the solution became completely depleted from soluble protein.…”