Multistep protein transport across nanopores: description and prediction

In voltage driven translocation experiments (Kasianowicz et al. 1996),an applied voltage across two electrolytic cells connected through ananopore induces the migration of macromolecules across the hole. The macromolecule engaging the pore produces detectable ion current variations that can be very informative on the physical and chemical properties of the passing species. While this experimental technique is announced to work for fast and cheap sequencing of nucleic acids, its applicability to protein molecules is still under intensive research.</p><p>An increasing accumulation of experimental data supports the view that large proteins translocate across narrow pores via a multistep process involving a sequence of dynamical bottlenecks (stall events) that, to some extent, can be considered as the fingerprint of the passing molecule. Our computer simulations on a coarse-grained model of the protein-pore system confirm the multistep scenario which results from the tight coupling between the unfolding process and the translocation dynamics. Moreover our results strongly indicate a correlation between :i) stall events of the transport dynamics, ii) ascending ramps in the free-energy profile G(Q) of a translocation reaction coordinate Q, and iii) regions of the protein richer in "back ward native-contacts" (i.e. native non-bonded interactions among those amino acids that have not yet entered the pore). ...