Molecular Binding in Supramolecular Fibrillar Biomolecules

Amyloid-β (Aβ) fibrils are biopolymer structures associated with the onset of Alzheimer's disease. Quantitative analyses of the interactions between Aβ fibrils and ligands, including dissociation constant (K_d) and binding stoichiometry (n), are crucial. In this paper, two independent-variable binding assays were simultaneously fitted to determine the K_d and n values of ruthenium(II) dipyridophenazine complex binding to Aβ fibrils. This approach eliminates the inherent ambiguity caused by the strong correlation between K_d and n in the binding equation. We demonstrate that this method is applicable to the quantitative binding study of other biopolymers with heterogeneous binding sites, such as calf thymus DNA (ct-DNA). Our method provides a robust evaluation of binding parameters in biopolymers with periodic systems (e.g. amyloids, DNA, and collagen), yielding precise K_d and n values, particularly when the concentration of binding sites is an unknown parameter.