Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor

The nicotinic acetylcholine receptor (nAChR) is a key molecule involved in the propagation of signals in the central nervous system and peripheral synapses. Although numerous computational and experimental studies have been performed on this receptor, the structural dynamics of the receptor underlying the gating mechanism is still unclear. To address the mechanical fundamentals of nAChR gating, both conventional molecular dynamics (CMD) and steered rotation molecular dynamics (SRMD) simulations have been conducted on the cryo-electron microscopy (cryo-EM) structure of nAChR embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer and water molecules. A 30-ns CMD simulation revealed a collective motion amongst C-loops, M1, and M2 helices. The inward movement of C-loops accompanying the shrinking of acetylcholine (ACh) binding pockets induced an inward and upward motion of the outer β-sheet composed of β9 and β10 strands, which in turn causes M1 and M2 to undergo anticlockwise motions around the pore axis. Rotational motion of the entire receptor around the pore axis and twisting motions among extracellular (EC), transmembrane (TM), and intracellular MA domains were also detected by the CMD simulation. Moreover, M2 helices undergo a local twisting motion synthesized by their bending vibration and rotation. The hinge of either twisting motion or bending vibration is located at the middle of M2, possibly the gate of the receptor. A complementary twisting-to-open motion throughout the receptor was detected by a normal mode analysis (NMA). To mimic the pulsive action of ACh binding, nonequilibrium MD simulations were performed by using the SRMD method developed in one of our laboratories. The result confirmed all the motions derived from the CMD simulation and NMA. In addition, the SRMD simulation indicated that the channel may undergo an open-close (O ↔ C) motion. The present MD simulations explore the structural dynamics of the receptor under its gating process and provide a new insight into the gating mechanism of nAChR at the atomic level.Author Summary: Nicotinic acetylcholine receptors (nAChRs) play an essential role in the propagation of signals in the central nervous system and peripheral synapses. However, their gating mechanism is still not fully understood. The cryo-EM structure of nAChRs provides a clue, but the dynamics of receptor structure remains to be elucidated. Using conventional molecular dynamics (CMD), normal mode analysis, and nonequilibrium MD techniques, we investigated the mechanical fundamentals of nAChR gating. Through the simulations, we detected the collective motions of the ligand-binding sites, extracellular (EC) domain, transmembrane (TM) domain, and intracellular (MA) domain, which together synthesize a local twisting motion of the M2 helices. To mimic the pulsive action of ligand binding, rotational motion of the receptor was simulated with the steered rotation MD (SRMD), a nonequilibrium MD method developed by us. The results indicate that the channel may undergo an open–close motion along with the rotation of the EC domain. Our study provides a clear picture of the correlation between the structural dynamics of nAChR and its gating mechanism.