Protein transport across nanopores: a statistical mechanical perspective from coarse-grained modeling and approaches

Protein Pept Lett. 2014 Mar;21(3):227-34. doi: 10.2174/0929866521666131227160550.

Abstract

We survey the transport of proteins across nanopores in the framework of coarse-grained modeling. The advantage of a reduced complexity with respect to full-atomistic techniques lies in the possibility of massive sampling of events, thus allowing a statistical mechanical description of translocation in terms of ensemble averages. Often, protein transport through narrow channels tightly couples with unfolding pathways causing a richer phenomenology compared to unstructured polymer translocation. This reflects into a process controlled by the presence of protein-specific free-energy barriers which can be conveniently estimated by statistical mechanical methods implemented in coarse-grained simulations. We illustrate how protein transport dynamics can be characterized by the statistical properties of trajectories and sometimes interpreted as driven diffusion of a single collective coordinate over a free-energy landscape. We also discuss, through selected examples, the connection between reduced-model simulations and recent experimental results.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Computer Simulation
  • Humans
  • Mechanical Phenomena
  • Models, Biological
  • Molecular Dynamics Simulation
  • Nanopores* / ultrastructure
  • Protein Conformation
  • Protein Transport
  • Proteins / chemistry
  • Proteins / metabolism*

Substances

  • Proteins