title: Multiple Proton Confinement in the M2 Channel from the Influenza A Virus.
abstract: The tetrameric M2 protein bundle of the influenza A virus is the proton channel responsible for the acidification of the viral interior, a key step in the infection cycle. Selective proton transport is achieved by successive protonation of the conserved histidine amino acids at position 37. A recent X-ray structure of the tetrameric transmembrane (TM) domain of the protein (residues 22-46) resolved several water clusters in the channel lumen, which suggest possible proton pathways to the His37 residues. To explore this hypothesis, we have carried out molecular dynamics (MD) simulations of a proton traveling towards the His37 side chains using MD with classical and quantum force fields. Diffusion through the first half of the channel to the "entry" water cluster near His37 may be hampered by significant kinetic barriers due to electrostatic repulsion. However, once in the entry cluster, a proton can move to one of the acceptor His37 in a nearly barrierless fashion, as evidenced both by MD simulations and a scan of the potential energy surface (PES). Water molecules of the entry cluster, although confined in the M2 pore and restricted in their motions, can conduct protons with a rate very similar to that of bulk water.
authors.affiliation: Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122-6078.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Carnevale
authors.forename: Giacomo
authors.initials: G
authors.lastname: Fiorin
authors.forename: Benjamin G
authors.initials: BG
authors.lastname: Levine
authors.forename: William F
authors.initials: WF
authors.lastname: Degrado
authors.forename: Michael L
authors.initials: ML
authors.lastname: Klein