FisMat2017 - Submission - View

Abstract's title: Frequency-control of protein translocation across an oscillating nanopore
Submitting author: Fabio Cecconi
Affiliation: Istituto dei Sistemi Complessi (CNR)
Affiliation Address: Via dei Taurini 19, 00185 Rome
Country: Italy
Oral presentation/Poster (Author's request): Oral presentation
Other authors and affiliations: M.A. Shahzad (Dipartimento di Fisica, Università di Camerino, Italy), U. Marini Bettolo Marconi (Dipartimento di Fisica, Università di Camerino,Italy), Angelo Vulpiani (Dipartimento di Fisica, Università “Sapienza” di Roma, Italy)
Abstract

 

 

The discovery that biological and solid-state nanoscale pores can be employed as molecular sensors has attracted great interest and stimulated a certain body of research focused on development of "nano-sensing" devices.

The operational performance of such devices is known to depend on the possibility to control the rates at which the molecules to be analyzed cross the nanopores. 
This issue becomes a bottleneck when nanopores are supposed to work as  high-throughput sequencing tools for large biopolymers (DNA, proteins).  
In this perspective, we will discuss how the transport of a lipid binding protein (LBP) across a nanopore can be controlled at molecular level by applying a vibration to the nanopore structure. The problem is studied using a phenomenological coarse-grained computational model that simplifies both protein chain and pore geometry. 
We investigate, via molecular dynamics, the interplay between transport and unfolding when the section of the nanopore oscillates periodically in time with a certain frequency (Radial Breathing Mode). 
We find that when the LPB is mechanically pulled into the vibrating nanopore exhibits a translocation dynamics which 
in some frequency range is accelerated and shows a frequency locking to the pore dynamics. 
The main effect of pore RBM is the suppression of stalling events of the translocation dynamics, hence, 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.