Theoretical study of potential ion-channels formed by a bundle of alpha-helices: effect of the presence of polar residues along the channel inner wall.

In a channel-forming bundle of five alpha-helices of poly-L-alanine, the replacement of all the alanyl side-chains lining the inner wall by serines is shown, by energy optimization, to produce only small modifications of the packing. The stability of the bundle is larger than that of the pure alanyl package, owing to hydrogen bonding between serine hydroxyls and carbonyl oxygens. The energy profile for sodium as well as the water-channel interactions are favored by the presence of the OH groups and by the lability of the seryl side chains. The possible general significance of the results is suggested.