Nanopores as biosensors: sequencing and theoretical challenges

Fabio Cecconi, Marco Bacci, Mauro Chinappi, Carlo Massimo Casciola

Istituto dei Sistemi Complessi (ISC-CNR), Rome, Italy

In voltage-driven translocation experiments, an applied voltage across two electrolytic cells connected through a nanopore induces the migration of proteins and other macromolecules across the nanopore. A macromolecule engaging the pore produces detectable ion-current variations very informative on its physical-chemical properties [1]. An increasing accumulation of data [2,3] supports the view that protein translocation across narrow pores is a multistage process characterized by a sequence of dynamical “stall events” (bottlenecks) representing, to some extent, the fingerprint of the passing molecule. We analyze, via molecular dynamics simulations on a coarse-grained model of the protein-pore system, the occurrence of the multistage scenario resulting from the tight coupling between transport and unfolding.

Simulations strongly indicate a relationship between:

We thus argue that a nontrivial inference on the presence of a multistep translocation dynamics can be done from the knowledge of the protein native-state topology. One theoretical challenge is reconstructing the structural properties of proteins from the information conveyed by their multistage dynamics across narrow nanopores [4].

References

  1. L.Movileanu “Interrogating single proteins through nanopores: challenges and opportunities” Trends Biotechnol. 27, 333 (2009).
  2. J.Nivala, D.B.Marks and M.Akeson “Unfoldase mediated protein translocation through and alpha-hemolysin nanopore” Nat. Biotech. 31, 247 (2013).
  3. D.Rodriguez-Larrea and H.Bayley “Multistep protein unfolding during nanopore translocation” Nat Nanotechnol. 8, 288 (2013).
  4. H.W.de-Haan and G.W.Slater, “Translocation of Rod-Coil Polymers: Probing the Structure of Single Molecules within Nanopores”, Phys. Rev. Lett. 110, 048101 (2013).