Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A

Proton transfer in biological systems is thought to often proceed through hydrogen-bonded chains of water molecules. The ion channel, gramicidin A (gA), houses within its helical structure just such a chain. Using the density functional theory based ab initio molecular dynamics Car-Parrinello method, the structure and dynamics of proton diffusion through a polyglycine analog of the gA ion channel has been investigated. In the channel, a proton, which is initially present as hydronium (H3O+), rapidly forms a strong hydrogen bond with a nearest neighbor water, yielding a transient H5O2+ complex. As in bulk water, strong hydrogen bonding of this complex to a second neighbor solvation shell is required for proton transfer to occur. Within gA, this second neighbor shell included not only a channel water molecule but also a carbonyl of the channel backbone. The present calculations suggest a transport mechanism in which a priori carbonyl solvation is a requirement for proton transfer.