Revisiting the Origin of Nanopore Current Blockage for Volume Difference Sensing at the Atomic Level

Abstract

Changes in the nanopore ionic current during entry of a target molecule underlie the sensing capability and dominate the intensity and extent of applications of the nanopore approach. The volume exclusion model has been proposed and corrected to describe the nanopore current blockage. However, increasing evidence shows nonconformity with this model, suggesting that the ionic current within a nanopore should be entirely reconsidered. Here, we revisit the origin of nanopore current blockage from a theoretical perspective and propose that the noncovalent interactions between a nanopore and a target molecule affect the conductance of the solution inside the nanopore, leading to enhanced current blockage. Moreover, by considering the example of an aerolysin nanopore discriminating the cytosine DNA and methylcytosine DNA that differ by a single methyl group, we completely demonstrate, by nanopore experiments and molecular dynamics simulations, the essential nature of this noncovalent interaction for discrimination. Our conductance model suggests multiplicative effects of both volume exclusion and noncovalent interaction on the current blockage and provides a new strategy to achieve volume difference sensing at the atomic level with highly specific current events, which would promote the nanopore protein sequencing and its applications in real-life systems.

Enhanced identification of Tau acetylation and phosphorylation with an engineered aerolysin nanopore

“…Previous works verified that non‐covalent interactions between the nanopore sensing interfaces and targets could be manipulated to support accurate distinction of peptides/proteins [23,31,32]. Recently, a study demonstrated theoretically and experimentally the possibility of non‐covalent interactions between a nanopore and analytes in regulating the current blockages [33]. Several available strategies were proposed to decelerate translocation speeds of peptides/proteins to acquire the nanopore current recording at high signal‐to‐noise ratios [24,34–37].…”

An engineered third electrostatic constriction of aerolysin to manipulate heterogeneously charged peptide transport

“…According to our previous studies, the R1 constricted region (T218 ∼ D222 and T274 ∼ S278) at the entrance of AeL determines the selectivity of the nanopore. 27–31 The introduction of charged residues at R1 achieved a charge selective AeL sensor. 32…”

Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin

“…Another major difference among the channels is the value of the parameter $${E_b}$$. As discussed previously, the simplest interpretation of this empirical parameter is the membrane binding energy of αSyn; however, the value of $${E_b}$$ can also be affected by anomalously slow unbinding kinetics introduced by disordered membrane binding domains [24], as well as by electrostatic or chemical association between the polyanionic C‐terminal domain and the net positively charged VDAC pore lumen [1, 63, 64]. Of these, only the latter is clearly channel‐specific and suggests a difference in the pore/polypeptide association energy between VDAC/αSyn and MspA/αSyn of about $$7\;{k_B}T$$.…”