Multi-Tier Models of Protein Action

Abstract

The role of protein relaxation in protein action has been modeled as a bounded diffusion process, involving a single Smoluchowski equation with a sink term. This is insufficient when the ligand within the protein, or the active site, can have multiple states. Examples are the states of the active site of an enzyme, such as cholesterol oxidase (unbound, bound, reduced) or the ligand location within myoglobin. To treat such situations, we consider multi-tier bounded-diffusion models, which involve coupled Smoluchowski equations for harmonic potentials with appropriate sink terms.