Frequency-control of protein translocation across an oscillating nanopore

TL;DR

This study uses computational modeling to explore how oscillating nanopores can control and accelerate protein translocation, revealing frequency-dependent effects that can optimize transport efficiency.

Contribution

It introduces a coarse-grained simulation approach to analyze protein translocation through vibrating nanopores, highlighting the role of pore oscillation frequency in controlling transport dynamics.

Findings

Oscillating nanopores can accelerate protein translocation.

Frequency tuning suppresses stalling events during transport.

Translocation dynamics can be understood via driven-diffusion theory.

Abstract

The translocation of a Lipid Binding Protein (LBP) is studied using a phenomenological coarse-grained computational model that simplifies both chain and pore geometry. We investigated via molecular dynamics the interplay between transport and unfolding in the presence of a nanopore whose section oscillates periodically in time with a frequency omega, a motion often referred to as radial breathing mode (RBM). We found that the LPB when mechanically pulled into the vibrating nanopore exhibits a translocation dynamics that in some frequency range is accelerated and shows a frequency locking to the pore dynamics. The main effect of pore vibrations is the suppression of stalling events of the translocation dynamics, hence, a proper frequency tuning allows both regularization and control of the overall transport process. Finally, the interpretation of the simulation results is easily achieved by resorting to a first passage theory of elementary driven-diffusion processes.