Decrypting the Sequence of Structural Events during the Gating Transition of Pentameric Ligand-Gated Ion Channels Based on an Interpolated Elastic Network Model

Despite many experimental and computational studies of the gating transition of pentameric ligand-gated ion channels (pLGICs), the structural basis of how ligand binding couples to channel gating remains unknown. By using a newly developed interpolated elastic network model (iENM), we have attempted to compute a likely transition pathway from the closed- to the open-channel conformation of pLGICs as captured by the crystal structures of two prokaryotic pLGICs. The iENM pathway predicts a sequence of structural events that begins at the ligand-binding loops and is followed by the displacements of two key loops (loop 2 and loop 7) at the interface between the extracellular and transmembrane domain, the tilting/bending of the pore-lining M2 helix, and subsequent movements of M4, M3 and M1 helices in the transmembrane domain. The predicted order of structural events is in broad agreement with the Φ-value analysis of α subunit of nicotinic acetylcholine receptor mutants, which supports a conserved core mechanism for ligand-gated channel opening in pLGICs. Further perturbation analysis has supported the critical role of certain intra-subunit and inter-subunit interactions in dictating the above sequence of events.Author Summary: Pentameric ligand-gated ion channels are a family of membrane proteins that open/close an ion-conducting channel in response to the binding of specific ligands. Some members of the family, including nicotinic acetylcholine receptors, play key physiological roles in signal transduction at synapses. Despite many experimental and computational studies of the gating transition of these pentameric ion channels, the structural basis of how ligand binding couples to channel opening remains uncertain. In particular, the all-atom computer simulation of the gating transition is limited to nanosecond ∼ microsecond time scales while the entire transition takes tens of microseconds. In this study, we have employed a highly efficient coarse-grained modeling method to dissect the sequence of structural events underlying the gating transition. The model predictions are in broad agreement with the kinetic analysis of mutants of nicotinic acetylcholine receptors. This study has established a useful computational framework to simulate the functional dynamics of pentameric ligand-gated ion channels.