Thermodynamic landscapes of conformational regulation during intrinsically disordered protein fibrillation

Amyloid fibrillation of intrinsically disordered proteins (IDPs) involves a disorder-to-order transition driven by complex sequence-dependent interactions. However, how amino acid sequences and conformational ordering reshape the multi-chain free-energy landscape during fibril formation remains poorly understood. Here, we combine the hybrid-resolution coarse-grained HyRes model with umbrella sampling to reconstruct the potentials of mean force governing successive stages of IDP fibrillation, including free-chain association, fibril-surface recruitment, and multilayer fibril growth. Using α-synuclein, transactive response DNA-binding protein of 43 kDa (TDP-43), and a fibrillar-core construct of fused in sarcoma (FUS-FC) as representative amyloid-forming IDPs, we demonstrate that sequence-encoded electrostatic interactions are a major determinant of association free energies. α-Synuclein exhibits the strongest attraction and salt sensitivity, whereas TDP-43 shows weaker electrostatically regulated interactions. Association of the isolated FUS fibrillar core remains thermodynamically unfavorable, whereas inclusion of nonfibrillar regions makes association favorable. Charge-neutralization simulations further reveal the critical role of electrostatics and charge patterning in controlling association. Conformational restraints and fibrillar surface organization further modulate the free-energy landscape in a protein-specific manner, with recruitment governed by the accessibility and arrangement of surface interaction sites rather than fibril thickness alone. These results provide a thermodynamic framework connecting sequence, conformation, and surface organization to the molecular mechanisms of amyloid assembly.