Translational Mobilities of Proteins in Nanochannels: A Coarse-Grained Molecular Dynamics Study

TL;DR

This study uses coarse-grained non-equilibrium molecular dynamics simulations to analyze how proteins move through nanopores, revealing how confinement and force affect translation times and providing insights for nanopore design.

Contribution

It compares non-equilibrium and equilibrium CG simulations of protein translocation, highlighting effects of nanopore size and external force on mobility.

Findings

Translation time increases significantly as nanopore radius approaches protein size.

Good agreement between simulation results and biased diffusion model.

Insights for designing nanopores to control biomolecule motion.

Abstract

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.