Peptide nanotubes are widely studied for their potential application as efficient artificial ion channels. As peptide nanotubes can be found in the form of bundles, this paper proposes mathematical models for the interaction between peptide nanotubes in the bundles and the interaction of an ion with the bundle. These models describe the stable configuration of peptide nanotube bundles and the encapsulation of an ion into the bundle. We utilize the Coulomb’s law and the Lennard-Jones potential together with a continuum approach assuming that the atoms are smeared uniformly over the peptide nanotubes providing an average atomic density to obtain the interaction energy. Our result shows that there is an optimal bundle radius for each size of bundle, which gives rise to a stable bundle structure. The optimum distance between two nanotubes in the bundle of cyclo[(L-Gln-D-Ala)₃] is found to be approximately 22.48Å, which is in agreement with a recent molecular dynamics study. We also find that various sizes of bundle will accept an ion. However, a bundle comprising three peptide nanotubes represents an ideal ion channel as it optimizes the interaction between the ion and the bundle.

peptide nanotubes, nanotube bundles, Coulomb potential, Lennard-Jones potential, van der Waals interaction, ion channels.