Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors

Prabhat Tripathi, Liang Shuai, Himanshu Joshi, Hirohito Yamazaki, William H. Fowle, Aleksei Aksimentiev, Hicham Fenniri, and Meni Wanunu
Journal of the American Chemical Society 142(4) 1680-1685 (2020)
DOI:https://doi.org/10.1021/jacs.9b10993  BibTex

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Rosette nanotubes (RNTs) are a class of materials formed by molecular self-assembly of a fused guanine−cytosine base (G^C base). An important feature of these self-assembled nanotubes is their precise atomic structure, intriguing for rational design and optimization as synthetic transmembrane porins. Here, we present experimental observations of ion transport across 1.1 nm inner diameter RNT porins (RNTPs) of various lengths in the range 5−200 nm. In a typical experiment, custom lipophilic RNTPs were first inserted into lipid vesicles; the vesicles then spontaneously fused with a planar lipid bilayer, which produced stepwise increases of ion current across the bilayer. Our measurements in 1 M KCl solution indicate ion transport rates of ~50 ions s-1 V-1 m, which for short channels amounts to conductance values of ~1 nS, commensurate with naturally occurring toxin channels such as α-hemolysin. Measurements of interaction times of α-cyclodextrin with RNTPs reveal two distinct unbinding time scales, which suggest that interactions of either face of α-cyclodextrin with the RNTP face are differentiable, backed with all-atom molecular dynamics simulations. Our results highlight the potential of RNTPs as self-assembled nonproteinaceous single-molecule sensors and selective nanofilters with tunable functionality through chemistry.

Abstract

Rosette nanotubes (RNTs) are a class of materials formed by molecular self-assembly of a fused guanine−cytosine base (G^C base). An important feature of these self-assembled nanotubes is their precise atomic structure, intriguing for rational design and optimization as synthetic transmembrane porins. Here, we present experimental observations of ion transport across 1.1 nm inner diameter RNT porins (RNTPs) of various lengths in the range 5−200 nm. In a typical experiment, custom lipophilic RNTPs were first inserted into lipid vesicles; the vesicles then spontaneously fused with a planar lipid bilayer, which produced stepwise increases of ion current across the bilayer. Our measurements in 1 M KCl solution indicate ion transport rates of ~50 ions s-1 V-1 m, which for short channels amounts to conductance values of  ~1 nS, commensurate with naturally occurring toxin channels such as α-hemolysin. Measurements of interaction times of α-cyclodextrin with RNTPs reveal two distinct unbinding time scales, which suggest that interactions of either face of α-cyclodextrin with the RNTP face are differentiable, backed with all-atom molecular dynamics simulations. Our results highlight the potential of RNTPs as self-assembled nonproteinaceous single-molecule sensors and selective nanofilters with tunable functionality through chemistry.

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A side view of the 200 ns long MD simulation trajectory of the simulated system containing 0.6 M NaCl, showing the transmembrane transport of Na+ ions (yellow spheres) ions and Cl- ions (cyan spheres) through the RNT porin (shown in the light-red transparent surface). The lipid molecules are shown using thin lines. Water is not shown for the sake of clarity.

Top view of the 200 ns long MD simulation trajectory of the simulated system containing  0.6 M NaCl, showing the transmembrane transport of Na+ ions (yellow spheres) and Cl- ions (cyan spheres) through the RNT porin (shown in the light-red transparent surface). The lipid molecules are shown using thin lines.  Water is not shown for the sake of clarity. Only Na+ ions permeate through the central cavity whereas the Cl- ions prefer to bind to the outer region of the RNT porin i.e. in between the bases and porphyrins.

A side view of the 100 ns all-atom MD simulation trajectory of the system containing 0.6 M KCl, showing the transmembrane transport of K+ ions (tan spheres) and Cl- ions (cyan spheres) through the RNT porin (shown in the light-red transparent surface). The lipid molecules are shown using thin lines. Water is not shown for the sake of clarity.

Top view of the 100 ns long all-atom MD simulation trajectory of the system containing  0.6 M KCl, showing the transmembrane transport of K+ ions (tan spheres)  and Cl- ions (cyan spheres) through the RNT porin (shown in the light-red transparent surface). The lipid molecules are shown using thin lines.  Water is not shown for the sake of clarity. Only K+ ions permeate through the central cavity, Cl- ions prefer to bind/permeate the outer region of the RNT porin i.e. in between the bases and porphyrins.