Translational mobilities of proteins in nanochannels: A coarse-grained molecular dynamics study

We investigated the translation of a protein through model nanopores using coarse-grained (CG) nonequilibrium 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, r_{h}/r_{p}→1 (where r_{h} is the hydrodynamic radius of protein and r_{p} is the pore radius), the translation times are observed to increase by two orders of magnitude. The translation times are found to be in good agreement with the one-dimensional biased diffusion model. The results presented in this paper provide useful insights on nanopore designs intended to control the motion of biomolecules.