Small molecule ensembles reshape amyloid aggregation landscapes

Abstract

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 A{beta}42 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 A{beta}42 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. SignificanceAn emerging view of protein function recognizes that proteins exist as dynamic networks of interconverting conformational and aggregation states. Binding interactions and environmental perturbations remodel these networks, thereby altering protein behavior. Amyloid aggregates associated with Alzheimers disease exemplify such dynamic systems, yet how small molecules remodel them remains poorly understood. Using A{beta}42 as a model, we show that small molecules remodel amyloid networks by redistributing protein populations in a concentration-dependent manner. This redistribution is modulated by self-association of the small molecule, molecular crowding, and temperature. These findings establish population redistribution within dynamic amyloid networks as a mechanism for remodeling protein assemblies, offering new insights into controlling pathological aggregation.