Translocation Mobilities of Proteins in Nanopores: A Coarse-Grained Molecular Dynamics Study.
We investigate the translocation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compare the results with a continuum model. We considered the effects of nanopore confinement and external force on the translocation of streptavidin through nanopores of dimensions representative of experiments. As the nanopore radius approaches the protein hydrodynamic radius, the translocation times are observed to increase by 3 to 4 orders of magnitude. The mobilities are found to be in reasonable agreement with the prediction from Einstein-Smoluchowski relation where the diffusion coefficient was obtained from EMD simulations. The translocation times are found to be in good agreement with one-dimensional biased diffusion model. The results presented in this paper serve in rationalizing the experimental observations and provide strategic guidelines on choosing parametric conditions for applications such as protein sensors.
Publisher URL: http://arxiv.org/abs/1801.08697
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