Multisite Binding in Two and Three Dimensions

Abstract

We recently studied the role of diffusion on the kinetics of ligand binding to a macromolecule with inequivalent sites [J. Chem. Phys.; v. 150, 094104 (2019)]. We found that in the simplest possible description, it is not sufficient to simply renormalize the rate constants of chemical kinetics, but one must introduce direct transitions between the bound states in the kinetic scheme. The physical reason for this is that a ligand that just dissociated from one site can directly rebind to the other rather than diffuse away into the bulk. Such a simple description is not valid in two dimensions because a ligand can never diffuse away into the bulk. In this work, we consider a variety of more sophisticated implementations of our general theory [J. Phys. Chem. B; v. 122, 11338-11354 (2018)] that are valid in both two and three dimensions. We compare the predicted time dependence of the concentrations for a wide range of parameters and establish the range of validity of various levels of the general theory.