Ligand binding to transiently accessible sites: mechanisms for varying apparent binding rates

Many biological processes are characterized by models where ligand has continuous access to binding sites. Use-dependent processes such as ion channel blockade appear to represent a class of processes where binding site access is transient and is dependent on channel conformation (state). (Alternatively, the existence of a proper conformation for binding might be transient.) We assume binding takes place only with a site that is accessible or in a bindable conformation. For ion channels, channel conformation responds to local chemical or electrical stimulation. The stimulus amplitude determines the mixture of channels with accessible and inaccessible sites. When conformation equilibrium is achieved rapidly in relation to ligand binding, then ligand binding can be considered the result of an apparent binding rate determined by the true binding rate as modified by the fraction of accessible sites. With repetitive stimulation, the continuous access model can be extended to a setting where apparent binding rates repetitively switch in response to the stimulus induced variation in mixture of site states. The resulting theoretical description provides a means for relating equilibrium binding parameters with those obtained under conditions of repetitive stimulation. In particular: (1) binding is piecewise exponential; (2) the envelope of binding measured at each pulse in a train varies exponentially with an apparent rate linearly dependent on the mixture specific rates; and (3) the steady state degree of binding site saturation is linearly dependent on the mixture specific equilibria.