  We investigated the translation of a protein through model nanopores using
coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and
compared the mobilities with those obtained from previous coarse-grained
equilibrium molecular dynamics model. We considered the effects of nanopore
confinement and external force on the translation of streptavidin through
nanopores of dimensions representative of experiments. As the nanopore radius
approaches the protein hydrodynamic radius, the translation times are observed
to increase by 2 orders of magnitude. The translation times are found to be in
good agreement with one-dimensional biased diffusion model. The results
presented in this paper provide useful insights on nanopore designs intended to
control the motion of biomolecules.
