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A striking feature of the alpha-hemolysin channel—a prime candidate for biotechnological applications—is the dependence of its ionic conductance on the magnitude and direction of the applied bias. Through a combination of lipid bilayer single-channel recording and molecular dynamics (MD) simulations, we characterized the current-voltage relationship of alpha-hemolysin for all alkali chloride salts at neutral pH. The rectification of the ionic current was found to depend on the type of cations and increase from Li+ to Cs+. Analysis of the MD trajectories yielded a simple quantitative model that related the ionic current to the electrostatic potential, the concentration and effective mobility of ions in the channel. MD simulations reveal that the major contribution to the current asymmetry and rectification properties originates from the cationic contribution to the current that is significantly reduced in a cationic dependent way when the membrane polarity is reversed. The variation of chloride current was found to be less important. We report that the differential affinity of cations for the charged residues positioned at the channel’s end modulates the number of ions inside the channel stem thus affecting the current properties. Through direct comparison of simulation and experiment, this study evaluates the accuracy of the MD method for prediction of the asymmetric, voltage dependent conductances of a membrane channel.

The protein nanopore Mycobacteria smegmatis porin A (MspA), can be used to sense individual nucleotides within DNA, potentially enabling a technique known as nanopore sequencing. In this technique, single stranded DNA electrophoretically moves through the nanopore and results in an ionic current that is nucleotide-specific. However, with a high transport velocity of the DNA within the nanopore, the ionic current cannot be used to distinguish signals within noise. Through extensive (~100 μs in total) all-atom molecular dynamics simulations, we examine the effect of positively charged residues on DNA translocation rate and the ionic current blockades in MspA. Simulation of several arginine mutations show a ~10–30 fold reduction of DNA translocation speed without eliminating the nucleotide induced current blockages. Comparison of our results with similar engineering efforts on a different nanopore (alpha-hemolysin) reveals a non-trivial effect of nanopore geometry on the ionic current blockades in mutant nanopores.

Electric field-driven translocation of DNA strands through biological nanopores has been shown to produce blockades of the nanopore ionic current that depend on the nucleotide composition of the strands. Coupling a biological nanopore MspA to a DNA processing enzyme has made DNA sequencing via measurement of ionic current blockades possible. Nevertheless, the physical mechanism enabling the DNA sequence readout has remained undetermined. Here, we report the results of all-atom molecular dynamics simulations that elucidated the physical mechanism of ionic current blockades in the biological nanopore MspA. We find that the amount of water displaced from the nanopore by the DNA strand determines the nanopore ionic current, whereas the steric and base-stacking properties of the DNA nucleotides determine the amount of water displaced. Unexpectedly, we find the effective force on DNA in MspA to undergo large fluctuations, which may produce insertion errors in the DNA sequence readout.

We consider the properties of a self-avoiding polymer chain, adsorbed on a solid attractive substrate which is attached with one end to a pulling force. The conformational properties of such chain and its phase behavior are treated within a Grand Canonical Ensemble (GCE) approach. We derive theoretical expressions for the mean size of loops, trains, and tails of an adsorbed chain under pulling as well as values for the universal exponents which describe their probability distribution functions. A central result of the theoretical analysis is the derivation of an expression for the crossover exponent φ, characterizing polymer adsorption at criticality, φ = α − 1, which relates the precise value of φ to the exponent α, describing polymer loop statistics. We demonstrate that 1 − γ11 < α < 1 + ν, depending on the possibility of a single loop to interact with neighboring loops in the adsorbed polymer. The universal surface loop exponent γ11 ≈ −0.39 and the Flory exponent ν ≈ 0.59.We present the adsorption-desorption phase diagram of a polymer chain under pulling and demonstrate that the relevant phase transformation becomes first order whereas in the absence of external force it is known to be a continuous one. The nature of this transformation turns to be dichotomic, i.e., coexistence of different phase states is not possible. These novel theoretical predictions are verified by means of extensive Monte Carlo simulations.