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 (Kd) and binding stoichiometry (n), are crucial. In this paper, two independent-variable binding assays were simultaneously fitted to determine the Kd and n values of ruthenium(II) dipyridophenazine complex binding to Aβ fibrils. This approach eliminates the inherent ambiguity caused by the strong correlation between Kd 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 Kd and n values, particularly when the concentration of binding sites is an unknown parameter.