Breakdown of supersaturation barrier links protein folding to amyloid formation

Abstract

The thermodynamic hypothesis of protein folding, known as the “Anfinsen’s dogma” states that the native structure of a protein represents a free energy minimum determined by the amino acid sequence. However, inconsistent with the Anfinsen’s dogma, globular proteins can misfold to form amyloid fibrils, which are ordered aggregates associated with diseases such as Alzheimer’s and Parkinson’s diseases. Here, we present a general concept for the link between folding and misfolding. We tested the accessibility of the amyloid state for various proteins upon heating and agitation. Many of them showed Anfinsen-like reversible unfolding upon heating, but formed amyloid fibrils upon agitation at high temperatures. We show that folding and amyloid formation are separated by the supersaturation barrier of a protein. Its breakdown is required to shift the protein to the amyloid pathway. Thus, the breakdown of supersaturation links the Anfinsen’s intramolecular folding universe and the intermolecular misfolding universe.

Targeting DNA topoisomerases or checkpoint kinases results in an overload of chaperone systems, triggering aggregation of a metastable subproteome

“…Protein supersaturation refers to proteins that are expressed at high levels relative to their intrinsic propensity to aggregate, which makes them vulnerable to aggregation. Supersaturation has been shown to underlie the widespread protein aggregation observed in age-related neurodegenerative disease, and in general ageing (Ciryam et al 2015, 2019; Freer et al 2019; Kundra et al 2017; Noji et al 2021). The relevance of supersaturation is underlined by the notion that evolutionary pressures appear to have shaped proteomes along its lines, so that at a global level, protein abundance is inversely correlated with aggregation propensity (Tartaglia et al 2007).…”

Polyphenol‐solubility alters amyloid fibril formation of α‐synuclein

“…The phase diagrams consist of soluble and amyloid regions, and the region of amorphous aggregation. Although the amyloid region consists of a metastable region, where supersaturation persists without seeding or strong agitation, and a labile region, where spontaneous amyloid formation occurs after a lag time, 7,[53][54][55][56] we did not distinguish the two regions in this paper because the present experiments under ultrasonic radiation did not distinguish the reaction types. Moreover, we did not include the amorphous region for EGCG because αSN did not form amorphous aggregates under the present experimental conditions.…”

“…The conformational phase diagram is useful for representing crystallization and amorphous aggregation depending on the concentrations of proteins and additives. 7,48 A similar approach was employed in our previous studies, proposing phase diagrams of β 2microglobulin conformational states depending on NaCl, detergents, and/or heparin concentrations. 15,20,[42][43][44][45][46][47] Assuming that polyphenols also alter the solubility of proteins in order to inhibit or promote protein aggregation, 22,[49][50][51][52] we created phase diagrams of αSN dependent on the concentrations of αSN and polyphenols (Figure 7).…”

“…Amyloid fibrils are composed of a cross‐β structure, in which β‐strands align perpendicularly to fibril axis. Thus far, a large number of proteins and peptides, including those not associated with diseases, have been demonstrated to form amyloid fibrils 2–7 . Solid‐state NMR and recent cryo‐EM techniques clarified the overall atomic structures of amyloid fibrils for an increasing number of proteins and peptides 8–11 .…”

“…10,[12][13][14] From a traditional physicochemical viewpoint, amyloid fibril formation is a concentration-dependent phase transition of a solute occurring above solubility through a nucleation and elongation mechanism, which is similar to the crystallization of solutes. 7,15,16 In this context, it is assumed that protein solubility decreases or increases with an increase in the concentration of additives such as sodium sulfate. α-Synuclein (αSN), made of 140 amino acid residues and having an isoelectric point (pI) value of 4.7, is responsible for synucleinopathies, including Parkinson's disease, Lewy body disease, and multiple system atrophy.…”