Simulations of Higher-Order Protein Organizations Using a Fuzzy Framework

Figure 1

Schematic representation of the model system with one (a) and three interacting molecules (b). is the binding preference of a binding element (α), which is computed as the average of the residue-based binding affinities (equation (1)). is the dynamics of the linker (λ) with length , which is obtained as the average of the residue-based values (equation (5)). The local concentration of the available binding sites is computed within a volume , which is scaled by the linker dynamics (, equation (6)).

(a)

(b)