Figure 7. A conceptual framework to deconstruct nucleation barriers.

(A) Schematic intracellular protein phase diagram for Sup35, with concentration on x-axis and stress/acidity on y-axis (increasing from top to bottom). Blue shading also indicates concentration. The cell physiologically resides in the amyloid “A” regime, and yet endogenous Sup35 remains soluble over cellular timescales due to the large kinetic barrier to amyloid nucleation. Cells cross into the condensate “C” regime either upon exposure to stress (represented by travel downward) or upon experimental over-expression of Sup35 (horizontal travel).

(B) Schematic intracellular protein phase diagram that distinguish the dispersed “D”, condensate “C”, and amyloid “A” phases. The phase space for amyloid encompasses that of condensation resulting in absence of the latter at equilibrium. For clarity, coexisting phases are not illustrated.

(C) Energy landscape of phases as a function of the order parameters Density (on the x-axis) and Structural Order (on the y-axis) that distinguish the state of the protein within each phase. Contour lines describe free energy from low (blue) to high (red). Ridges between basins indicate nucleation barriers. In the absence of a pre-existing amyloid template in the cell, amyloid nucleation proceeds through metastable condensates, as illustrated by the arrow.

(D) Condensates can also be so stable as to increase the barrier to amyloid nucleation.

(E) Heterogeneous templates such as [PIN⁺] bias the conformational ensemble of dispersed species toward that of amyloid, leading to a reduced nucleation barrier for amyloid formation that enables nucleation without prior condensation.