Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model

Abstract

Nanopore sensing has emerged as a versatile approach to detection and identification of biomolecules. Presently, researchers rely on experience and intuition for choosing or modifying the nanopores to detect a target analyte. The field would greatly bene t from a computational method that could relate the atomic-scale geometry of the nanopores and analytes to the blockade nanopore currents they produce. Existing computational methods are either computationally too expensive to be used routinely in experimental laboratories or not sensitive enough to account for the atomic structure of the pore and the analytes. Here, we demonstrate a robust and inexpensive computational approach-the steric exclusion model (SEM) of nanopore conductance-that is orders of magnitude more efficient than all-atom MD and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. The method combines the computational efficiency of a finite element solver with the atomic precision of a nanopore conductance map to yield unprecedented speed and accuracy of ionic current prediction. We validate our SEM approach through comparison with the current blockades computed using the all-atom molecular dynamics method for a range of proteins confined to a solid-state nanopore, biological channels embedded in a lipid bilayer membranes and blockade currents produced by DNA homopolymers in MspA. We illustrate potential applications of SEM by computing blockade currents produced by nucleosome proteins in a solid-state nanopore, individual amino acids in MspA and by testing the effect of point mutations on amino acid distinguishability. We expect our SEM approach to become an integral part of future development of the nanopore sensing field. * These authors contributed equally to the manuscript Supplementary Information Available The following files are available free of charge: SI Wilson2019.pdf. Simulated dependence of KCl, K + and Cl − conductivity from the center of carbon, hydrogen, nitrogen, oxygen atoms; comparison of the nanopore currents computed using the resistor and SEM models; comparison of SEM and MD blockade currents in MspA done using nominal conductivity of KCl and for 3'-trans systems; supplementary methods detailing MD simulations of biological nanopores; and a table summarizing conditions for the biological nanopores simulations.

Nanopore‐Based Protein Sequencing Using Biopores: Current Achievements and Open Challenges

“…Hence, for similar amino acids dimensions, the charged residue give rise to a smaller blockade. Another recent computational work by Wilson et al, [123] compares the blockades of all 20 individual amino acids in MspA nanopore, reporting again volume-dependent blockades (i.e., blockade increases with volume), but not a significant charge effect. This work employs a reduced steric exclusion model to estimate the current blockades computing a 3D local conductivity map of the electrolyte inside the channel, based on the distance of each point from the nearest nonsolvent atom.…”

“…We recall that within a volume‐exclusion model (vide supra) and simplifying assumptions, [ 58,59 ] an electrically neutral analyte captured inside a cylinder‐like nanopore determines current blockades, Δ I blocked , directly proportional to the electrolyte volume excluded by the analyte (δ) (see also Figure 1, inset). [ 29 ] More accurate descriptions based on Poisson–Nernst–Planck equation, [ 21 ] Ohm law with local conductivities [ 123 ] and quasi‐1D models for pore resistance [ 124,125 ] have been developed for estimating the current blockade. In accordance to the scenario depicted in Figure 4I,b, Δ I blocked estimated for the “#” substate reflects the current blockade determined by a peptide captured inside the nanopore, precisely when a group of approximately three amino acids from the middle section of it occupies the constriction region of the α‐HL.…”

The emerging landscape of single-molecule protein sequencing technologies

“…All-atom molecular dynamics simulations using the α-hemolysin pores have demonstrated a global correlation between the volume of an amino acid and the current blockade in homopolymers 56 . Computationally efficient predictions using coarse-grained models have also performed well in comparison to all-atom molecular dynamics simulations for both solid-state and biological pores 57 .…”

Electrical Unfolding of Cytochrome c During Translocation Through a Nanopore Constriction

“…The average translocation time was found to exponentially depend on the pore diameter, Fig. 4E, whereas the maximum current blockade ratio (computed using SEM approach (66)) during the translocation, Fig. 4F, reached nearly 100% of the open pore current.…”