Can a Hydrophobic Pore Act as a Gate?
Recent near atomic-resolution of the nicotinic acetylcholine receptor (N. Unwin, personal communication) suggest that even when this ion channel is functionally closed the pore appears to be physically open. The aim of the project is to test whether a short/narrow pore between two water-filled cavities can act as a gate, and how this behaviour depends on the length, radius and hydrophobicity of the pore. The pore is modelled as a cylinder made from pseudo-atoms which is embedded in an octane slab, mimicking the situation of a channel protein in the lipid bilayer of the membrane. We are employing classical molecular dynamics in order to describe the motion of water molecules within and around the pore. Initial simulations suggest that water molecules do not penetrate a purely hydrophobic pore with the dimensions of the narrowest region of the pore in the closed conformation of the nAChR. Previous: Nicotinic Acetylcholine Receptor, Next: Viral Ion Channels, Up: Ion Channels, Return to: C
