(516x) Cooperative Binding Of Ligands To Biopolymers

The binding of ligands to sites on biopolymers is ubiquitous in living systems. Examples include (a) the binding of cofilin to actin filaments, (b) the binding of tPA to fibrin, and (c) the binding of transcription factors to DNA. The effects of cooperative binding on the dynamics of binding and clustering of ligands to a linear biopolymer were studied via a novel implementation of the stochastic simulation algorithm, wherein the kinetics of binding of ligands to monomers (or sites between monomers) are affected by the states of binding of next-door neighbors. An in-silico factorial experimental design - facilitated by high performance computing - was used to exhaustively characterize the thermodynamic and kinetic regimes in which cooperativity is experimentally discernable. Employing these results, a robust methodology was developed for the kinetic characterization of site-specific adsorption to linear biopolymers.