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

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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 qκ for binding (with a binding strength κ); except for the case of no binding κ ≤ 0 the presence of the chaperones gives rise to an effective force that drives the translocation process. In more detail, we develop a dynamical description of the process in terms of a (2+1)-variable master equation for the probability of having m monomers on the target side of the membrane with n bound chaperones at time t. Emphasis is put on the calculation of the mean first passage time as a function of total chain length M. The transfer coefficients in the master equation are determined through detailed balance, and depend on the relative chaperone size λ and binding strength κ, as well as the two rate constants k and q. The ratio γ ≤ q/k between the two rates determines, together with κ and λ, three limiting cases, for which analytic results are derived: (i) for the case of slow binding (), the motion is purely diffusive, and for large M; (ii) for fast binding () but slow unbinding (), the motion is, for small chaperones λ ≤ 1, ratchet-like, and ; (iii) for the case of fast binding and unbinding dynamics ( and ), we perform the adiabatic elimination of the fast variable n, and find that for a very long polymer , but with a smaller prefactor than for ratchet-like dynamics. We solve the general case numerically as a function of the dimensionless parameters λ, κ and γ, and compare to the three limiting cases.
Article numberS3945
JournalJournal of Physics: Condensed Matter
Issue number47
Publication statusPublished - 30 Nov 2005