Facilitated translocation of polypeptides through a single nanopore

Abstract

The transport of polypeptides through nanopores is a key process in biology and medicalbiotechnology. Despite its critical importance, the underlying kinetics of polypeptidetranslocation through protein nanopores is not yet comprehensively understood. Here, wepresent a simple two-barrier, one-well kinetic model for the translocation of short positivelycharged polypeptides through a single transmembrane protein nanopore that is equippedwith negatively charged rings, simply called traps. We demonstrate that the presence ofthese traps within the interior of the nanopore dramatically alters the free energylandscape for the partitioning of the polypeptide into the nanopore interior, as revealed bysignificant modifications in the activation free energies required for the transitions of thepolypeptide from one state to the other. Our kinetic model permits the calculation of therelative and absolute exit frequencies of the short cationic polypeptides througheither opening of the nanopore. Moreover, this approach enabled quantitativeassessment of the kinetics of translocation of the polypeptides through a proteinnanopore, which is strongly dependent on several factors, including the natureof the translocating polypeptide, the position of the traps, the strength of thepolypeptide–attractive trap interactions and the applied transmembrane voltage.