Pentameric ligand-gated ion channels belong to an important family of membrane proteins and play key roles in physiological processes. Based on the X-ray structure of prokaryotic pentameric ligand-gated ion channels from Gloebacter violaceus (GLIC), we performed a total of 1.05 µs coarse-grained molecular simulations, combining with atomic-level molecular simulation, and observed the pore closure and corresponding quaternary twist. We found that the pore closure by a concerted motion of rotating-tilting (toward the pore) of helices M2. Combining with previous experimental results, a model of describing the conformational transition for channel gating process is derived from our simulations: the top of the M2 helix occurs large conformational fluctuations, followed by a global conformational changes of the whole subunit|this process passes from one subunit to the neighbor one, finally, leading to the entire channel conformational changes, such as a “chain-reaction”.

Key words: pentameric ligand-gated ion channel, gating, coarse-grained