Directed motion emerging from two coupled random processes: Translocation of a chain through a membrane nanopore driven by binding proteins

Abstract

We investigate the translocation of a stiff polymer consisting of M monomers through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind onto the polymer, and partially prevent backsliding of the polymer through the pore. The process is characterized by the rates: k for the polymer to make a diffusive jump through the pore, q for unbinding of a chaperone, and the rate q kappa for binding (with a binding strength kappa); except for the case of no binding kappa=0 the presence of the chaperones give rise to an effective force that drives the translocation process. Based on a (2+1) variate master equation, we study in detail the coupled dynamics of diffusive translocation and (partial) rectification by the binding proteins. In particular, we calculate the mean translocation time as a function of the various physical parameters.

22 pages, 5 figures, IOP style

References in corpus (9)

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• Translocation Dynamics with Attractive Nanopore-Polymer Interactions
• Dynamics of DNA translocation through an attractive nanopore
• The chain sucker: translocation dynamics of a polymer chain into a long narrow channel driven by longitudinal flow
• Polymer translocation out of confined environments
• Polymer translocation under a pulling force: scaling arguments and threshold forces
• Master equation approach to DNA-breathing in heteropolymer DNA
• Dynamics of polymer translocation into a circular nanocontainer through a nanopore
• Chaperone-assisted translocation of flexible polymers in three dimensions
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• Exact steady-state velocity of ratchets driven by random sequential adsorption
• Translocation of stiff polymers through a nanopore driven by binding particles
• Fluctuations in Polymer Translocation
• Force-dependent diffusion coefficient of molecular Brownian ratchets
• Chaperone driven polymer translocation through Nanopore: spatial distribution and binding energy
• Mean velocity and effective diffusion constant for translocation of biopolymer chains across membrane
• Asymptotics of a Brownian ratchet for Protein Translocation