Theory of Diffusion-Limited Reactions between Proteins in a Confined Environment

Smoluchowski theory is extensively used to compute diffusion-limited reaction rates. It is based on the assumption that the reactants diffuse in from infinity. However, in many cases, this assumption fails for association reactions between biological macromolecules because they initially are confined inside a certain volume. Examples are association reactions between the linked subdomains of polyproteins, such as the Gag protein of HIV-1 and the assembly reactions of the molecular components of a virus in a "virus factories". Confinement greatly increases reaction rates. The talk will discuss how Smoluchowski's theory is generalized to include a confined environment by introducing particles at the finite range.