title: Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A.
abstract: 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.
authors.affiliation: Department of Chemistry, University of Pennsylvania, Philadelphia 19104, USA.
authors.forename: D E
authors.initials: DE
authors.lastname: Sagnella
authors.forename: K
authors.initials: K
authors.lastname: Laasonen
authors.forename: M L
authors.initials: ML
authors.lastname: Klein
mesh_terms: D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D006096:Gramicidin / Q000031:analogs & derivatives* / Q000737:chemistry; D006860:Hydrogen Bonding; D066298:In Vitro Techniques; D007473:Ion Channels / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011522:Protons; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D007473:Ion Channels; D010455:Peptides; D011522:Protons; D014867:Water; D006096:Gramicidin; C011080:polyglycine