Small-molecule-induced species redistribution drives amyloid remodeling along a conserved kinetic landscape

Proteins in living systems are highly dynamic, continuously populating heterogeneous ensembles of functionally distinct conformational and aggregation states whose relative populations and interconversion rates are governed by an underlying free-energy landscape. Perturbations such as ligand binding, chemical modification, or changes in the environment remodel these assemblies, thereby reshaping protein behavior and function. Understanding how such protein networks are dynamically remodeled is a fundamental challenge in biophysics. Here, we utilize the Aβ₄₂ aggregation landscape as a model to demonstrate that remodeling can occur without detectable changes in the apparent activation free-energy barrier, instead arising from system-level redistribution of species along a conserved kinetic pathway. Using EPPS (4-(2-hydroxyethyl)-1-piperazinepropanesulfonic acid) as a model modulator, temperature-dependent kinetic analysis reveals an invariant apparent activation free energy, suggesting that the underlying energetic framework remains unchanged even as the system is reshaped. We find that EPPS modulates Aβ₄₂ disaggregation in a concentration-dependent manner. At intermediate concentrations, enhanced redistribution toward soluble species is observed, whereas at higher concentrations, modulator self-association into supramolecular clusters is associated with reduced net disaggregation and partial recovery of aggregation signatures. Thermal disruption of these assemblies restores activity, consistent with a role of modulator self-association in governing the observed behavior. Furthermore, our experiments indicate that this disaggregation process is reduced in crowded environments compared to dilute conditions. Together, these results support a biophysical framework in which amyloid remodeling is driven by species redistribution along a conserved kinetic landscape, where the extent of disaggregation is determined by modulator concentration-dependent partitioning of protein species, modulator self-association, and environmental constraints.