title: Protein transport across nanopores: a statistical mechanical perspective from coarse-grained modeling and approaches.
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.
authors.forename: Fabio
authors.initials: F
authors.lastname: Cecconi
authors.forename: Marco
authors.initials: M
authors.lastname: Bacci
authors.affiliation: CNR-Istituto dei Sistemi Complessi, Via Dei Taurini 19, Roma, 00185, Italy. fabio.cecconi@roma1.infn.it.
authors.forename: Mauro
authors.initials: M
authors.lastname: Chinappi
mesh_terms: D000818:Animals; D003198:Computer Simulation; D006801:Humans; D055595:Mechanical Phenomena; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D058608:Nanopores / Q000648:ultrastructure; D011487:Protein Conformation; D021381:Protein Transport; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D011506:Proteins