Protein Transport Across Nanopores: A Statistical Mechanical Perspective From Coarse-Grained Modeling and Approaches

Author(s): Fabio Cecconi, Marco Bacci, Mauro Chinappi

Journal Name: Protein & Peptide Letters

Volume 21 , Issue 3 , 2014


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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.

Keywords: Coarse-grained Molecular Dynamics, Driven Diffusion Models, protein translocation, stalled conformations.

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Article Details

VOLUME: 21
ISSUE: 3
Year: 2014
Published on: 23 January, 2014
Page: [227 - 234]
Pages: 8
DOI: 10.2174/0929866521666131227160550
Price: $65

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