Chaperone assisted translocation

TL;DR

This paper models the translocation of stiff polymers through nanopores assisted by chaperones, analyzing how binding strength and valency influence the process using a detailed statistical mechanical approach.

Contribution

It introduces a comprehensive master equation model that accounts for multivalent chaperone binding and provides analytical and numerical insights into translocation dynamics.

Findings

Force depends on chaperone valency and binding strength.

Finite size corrections to the thermodynamic force are derived.

Mean translocation velocity varies with chaperone properties.

Abstract

We investigate the translocation of a stiff polymer through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind reversibly to the polymer on both sides of the membrane. A bound chaperone covers one (univalent binding) or many (multivalent binding) binding sites. Assuming that the diffusion of the chaperones is fast compared to the rate of translocation we describe the process by a one-dimensional master equation. We expand previous models by a detailed study of the effective force in the master equation, which is obtained by the appropriate statistical mechanical average over the chaperone states. The dependence of the force on the degree of valency (the number of binding sites occupied by a chaperone) is studied in detail. We obtain finite size corrections (to the thermodynamical expression for the force), which, for univalent binding, can be expressed analytically. We finally investigate the mean velocity for translocation as a function of chaperone binding strength and size. For both univalent and multivalent binding simple results are obtained for the case of a sufficiently long translocating polymer.