Potential of Mean Force Calculations for Ion Selectivity in a Cyclic Peptide Nanotube

the dehydration freeenergy barriers are not eliminated by an interaction between the anion and the peptide nanotube, leading to thehigh free energy barriers in the PMF profile. Calculations of the coordination numbers of the ions with oxygenatoms pertaining to either water molecules or carbonyl groups in the peptide nanotube reveal that thestabilization of the cations in the midplane regions of the nanotube arises from the favorable interaction of thecations with the negatively charged carbonyl oxygens.Key Words : Cyclic peptide nanotube, Ion selectivity, Molecular dynamics simulation, Potential of meanforce, Umbrella samplingIntroductionIon channels, which is a class of transmembrane proteins,have drawn great attention because they play a significantrole in nerve and muscle excitation, sensory transduction,and hormone secretion.