Molecular Dynamics Approach of Ion Channeling through Peptide Nanotubes

Abstract

We theoretically study the possibility of ion channeling through peptide nanotubes (PNTs). After designing the minimal peptide nanorings (PNRs) and their aggregated form (peptide nanotubes, PNTs) computationally, we carry out molecular dynamics (MD) calculations for cation channeling. Irrespective of the cation species (Li+, Na+, K+, or Mg2+), the present MD calculations show that cation channeling through PNTs occurs. Furthermore, inter-ring hydrogen bonds (HBs) survive and maintain the tubular form of PNTs during cation channeling. We introduce mobility such that cation channeling can be evaluated quantitatively. As the ion radius of the cation becomes smaller, the effective relaxation time τ (an order of pico sec) becomes larger. Accordingly, mobilities of 10-2–10-3 cm2/(V·s) are calculated. In contrast, when an anion (F-) passes through the PNTs, the inter-ring HBs are broken, thus inducing the breakdown of the peptide backbone. Consequently, H atoms from the broken HBs surround the channeling anion (F-) and halt its motion. For PNTs, cation channeling is preferred, while anion channeling does not occur.