Amyloid Aggregation and Liquid–Liquid Phase Separation from the Perspective of Phase Transitions

Abstract

Amyloid aggregation describes the aberrant selfassembly of peptides into ordered fibrils characterized by cross-β spine cores and is associated with many neurodegenerative diseases and Type 2 diabetes. Oligomers, populated during the early stage of aggregation, are found to be more cytotoxic than mature fibrils. Recently, many amyloidogenic peptides have been reported to undergo liquid−liquid phase separation (LLPS)�a biological process important for the compartmentalization of biomolecules in living cells�prior to fibril formation. Understanding the relationship between LLPS and amyloid aggregation, especially the formation of oligomers, is essential for uncovering disease mechanisms and mitigating amyloid toxicity. In this Perspective, available theories and models of amyloid aggregation and LLPS are first briefly reviewed. By drawing analogies to gas, liquid, and solid phases in thermodynamics, a phase diagram of protein monomer, droplet, and fibril states separated by coexistence lines can be inferred. Due to the high free energy barrier of fibrillization kinetically delaying the formation of fibril seeds out of the droplets, a "hidden" monomer-droplet coexistence line extends into the fibril phase. Amyloid aggregation can then be described as the equilibration process from the initial "out-of-equilibrium" state of a homogeneous solution of monomers to the final equilibrium state of stable amyloid fibrils coexisting with monomers and/or droplets via the formation of metastable or stable droplets as the intermediates. The relationship between droplets and oligomers is also discussed. We suggest that the droplet formation of LLPS should be considered in future studies of amyloid aggregation, which may help to better understand the aggregation process and develop therapeutic strategies to mitigate amyloid toxicity.

TDP-43 Promotes Amyloid-Beta Toxicity by Delaying Fibril Maturation via Direct Molecular Interaction

“…One of the critical early steps in amyloid fibril formation is the nucleation of short fibril seeds, which can then grow axially via monomer addition. The fibril seed represents a structural transition point between metastable oligomers and stable fibrils, and the growth of fibril seeds and ensuing secondary nucleation corresponds to the rapid elongation phase that is part of classical amyloid aggregation kinetics . By blocking the growth of fibril seeds, the lag phase can be extended, and fibril maturation delayed, and thus interaction with fibril seeds is a well-known mechanism of inhibiting fibrillization. − To further investigate how TDP-43 was capable of potently inhibiting Aβ fibrillization under substoichiometric conditions in vitro, we elected to simulate the NTD of TDP-43 with a short fibril seed.…”

Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations

“…The mechanisms of cross-β-amyloid self-assembly are the focus of intense research interest. , Amyloid self-assembly is a nucleation-dependent process characterized by an initial nucleation phase, during which prefibrillar oligomeric aggregates are formed, followed by an exponential growth phase wherein nuclei mature into fibrils by addition of monomer. Experimental kinetic and thermodynamic analyses have provided insight into these self-assembly processes, although the events that occur during the nucleation phase remain poorly understood. , These events are of particular importance in disease-relevant amyloid self-assembly since data indicates that prefibril oligomers may be the main toxic congeners in the related disorders. , The direct characterization of these early amyloid intermediates is challenging.…”

A reaction-diffusion model captures the essence of liquid-liquid phase separation

“…State-of-the-art experiments have greatly expanded our understanding of liquid-liquid phase separation (LLPS) processes and their intricacies [5][6][7][8][9][10][11]. However, a comprehensive physical grasp of LLPS remains a goal.…”