Computer Simulation of Ion Channel Gating: The M Channel of Influenza-A Virus in a Lipid Bilayer

Karl Schweighofer and Andrew Pohorille

Biophys. J., in press

Abstract:

The transmembrane fragment of the Influenza virus M protein forms a homotetrameric channel that transports protons. In this paper, we use molecular dynamics simulations to help elucidate the mechanism of channel gating by four histidines that occlude the channel lumen in the closed state. We test two competing hypotheses. In the ``shuttle'' mechanism, the nitrogen atom on the extracellular side of one histidine is protonated by the incoming proton and, subsequently, the proton on the nitrogen atom is released on the opposite side. In the "water-wire" mechanism, the gate opens due to electrostatic repulsion between four, simultaneously biprotonated histidines. This allows for proton transport along the water wire that penetrates the gate. For each system, composed of the channel embedded in a hydrated phospholipid bilayer, a 1.3 ns trajectory was obtained. It is found that the states containing single-protonated histindines in the or positions or one biprotonated residue, involved in the shuttle mechanism, are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfer. In contrast, the fully biprotonated state is not stable. Additional simulations show that if only two histidines are biprotonated the channel deforms but the gate remains closed. These results support the shuttle mechanism but not to the gate opening mechanism of proton gating in M.