The gramicidin A channel: theoretical energy profile computed for single occupancy by a divalent cation, Ca²⁺

The energy profile for the interaction of the divalent cation Ca²⁺ with the gramicidin A channel has been computed, introducing successively the different structural components of the channel, namely the polypeptide backbone, the ethanolamine tails and the amino acid side chains. The calculations have been performed in two fashions: (1) with the tail fixed in its most stable conformation, (2) with the tail allowed to optimize its conformation upon progression of the cation. The introduction of the tail and more particularly of its flexibility modifies considerably the profile. On the other hand, in both cases, the introduction of the side chains does not modify qualitatively the overall shape of the energy profile, although it brings about a general lowering of the energies. When the tail is mobile, a very deep and narrow minimum is found at 10.5 Å from the center and the central barrier is roughly 21 kcal/mol. The similarities and differences found with respect to the corresponding profiles for alkali ions, Na⁺ in particular, are discussed in connection with the very low permeability, if any, of gramicidin A for Ca²⁺.