Asymmetric Ligand Binding Facilitates Conformational Transitions in Pentameric Ligand-Gated Ion Channels

Abstract

The anesthetic propofol inhibits the currents of the homo-pentameric ligand-gated ion channel GLIC, yet the crystal structure of GLIC with five propofol molecules bound symmetrically shows an open-channel conformation. To address this dilemma and determine if symmetry of propofol binding sites affects the channel conformational transition, we performed a total of 1.5 As of molecular dynamics simulations for different GLIC systems with propofol occupancies of 0, 1, 2, 3, and 5. GLIC without propofol binding or with five propofol molecules bound symmetrically showed similar channel conformation and hydration status over multiple replicates of 100-ns simulations. In contrast, asymmetric binding to one, two or three equivalent sites in different subunits accelerated the channel dehydration, which was accompanied by increased conformational heterogeneity of the pore and shifted the lateral and radial tilting angles of the pore-lining TM2 towards a closed-channel conformation. The results differentiate two groups of systems based on the propofol binding symmetry. The difference between symmetric and asymmetric groups is correlated with the variance in the propofol-binding cavity adjacent to the hydrophobic gate and the force imposed by the bound propofol. Asymmetrically bound propofol produced greater variance in the cavity size that could further elevate the conformation heterogeneity. The force trajectory generated by propofol in each subunit over the course of a simulation exhibits an ellipsoidal shape, which has the larger component tangential to the pore. Asymmetric propofol binding creates an unbalanced force that expedites the channel conformation transitions. The findings from this study not only suggest that asymmetric binding underlies the propofol functional inhibition of GLIC, but also advocate for the role of symmetry breaking in facilitating channel conformational transitions.

Insights into Distinct Modulation of α7 and α7β2 Nicotinic Acetylcholine Receptors by the Volatile Anesthetic Isoflurane

“…More importantly, the result conveys the message that two or three subunits susceptible to anesthetics, such as ␤2 in ␣7␤2, are sufficient to produce functional effects. The message is consistent with the notion obtained from molecular dynamics simulations of anesthetic propofol action in GLIC (45).…”

Propofol Binding to the Resting State of the Gloeobacter violaceus Ligand-gated Ion Channel (GLIC) Induces Structural Changes in the Inter- and Intrasubunit Transmembrane Domain (TMD) Cavities

“…8D). Propofol docked in the intrasubunit cavity as previously observed crystallographically (1) and computationally (21,24). In addition, propofol was found in the intersubunit site under the M2-M3 loop though less frequently.…”

Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics

“…More recently, the characterization of both atomicresolution structure and anesthetic sensitivity in GLIC provided valuable new simulation templates. Multiple binding sites for halothane and isoflurane in GLIC have been computationally identified and predicted to disrupt the channel's quaternary structure (Chen et al, 2010;Willenbring et al, 2011;Mowrey et al, 2013) or block the pore (Lebard et al, 2012). The discovery of enhanced ethanol and anesthetic potentiation in the F149A variant of GLIC allowed more direct comparisons: 1-microsecond simulations showed selective intersubunit ethanol binding to ethanol-sensitized (F149A) receptors, along with expansion of the channel pore (Murail et al, 2012).…”