Molecular Dynamics Simulations of DNA within a Nanopore: Arginine−Phosphate Tethering and a Binding/Sliding Mechanism for Translocation

Abstract

Protein nanopores show great potential as low-cost detectors in DNA sequencing devices. To date, research has largely focused on the staphylococcal pore α-hemolysin (αHL). In the present study, we have developed simplified models of the wildtype αHL pore and various mutants, in order to study the translocation dynamics of single-stranded DNA under the influence of an applied electric field. The model nanopores reflect the experimentally measured conductance values in planar lipid bilayers. We show that interactions between rings of cationic amino acids and DNA backbone phosphates result in metastable tethering of nucleic acid molecules within the pore, leading us to propose a “binding and sliding” mechanism for translocation. We also observe folding of DNA into non-linear conformational intermediates during passage through the confined nanopore environment. Despite adopting non-linear conformations, the DNA hexamer always exits the pore in the same orientation as it enters (3′ to 5′) in our simulations. The observations from our simulations help to rationalize experimentally determined trends in residual current and translocation efficiency for αHL and its mutants.

The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin

“…To aid in such applications, molecular dynamics (MD) simulations are performed to make predictions of the expected current reduction from channel occlusion by a biomolecule compared to the background current across the open channel (20)(21)(22)(23)(24). However, MD simulations have not demonstrated the ability to accurately reproduce experimental data (i.e., channel ionic current), over relevant timescales even when utilizing multiple force fields (FFs) (20,21,23,25).…”

Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force

“…In that study, we identified the existence and significance of a phosphate‐lysine interaction. Bond et al have since verified this interaction in a separate study . They performed nucleotide translocation simulations through a simplified αHL pore using an applied transmembrane potential and determined that the phosphate‐lysine interaction plays a major role.…”

Modeling and Simulation of Ion Channels

“…635 Bond et al employed all-atom MD simulations to explore the translocation of short strands of DNA through a simplified model of the α -hemolysin pore comprising the stem of the pore surrounded by a membrane mimetic slab. 99 The study examined the effect of cationic amino acids on the translocation dynamics of DNA. Compared to wild type α -hemolysin, arginine mutations were found to reduce the transport rate of DNA through the pore, as well as the ionic current.…”