Does Symmetry of Ligand Occupancy Matter to Conformational Transitions of Pentameric Ligand Gated Ion Channels?

Abstract

For a homo-pentameric ligand gated ion channel, agonist occupancy of only two or three of the five possible binding sites has been found to produce the maximal channel response. Does asymmetric ligand binding also apply for channel antagonism? The anesthetic propofol inhibits the homo-pentameric GLIC, but the crystal structure of GLIC bound symmetrically with propofol to each of the five binding sites shows a virtually identical open channel as the one without drug binding. We hypothesize that symmetric ligand occupancy of all five binding sites may not occur under physiological conditions, and asymmetric ligand binding facilitates channel conformational changes? To test this hypothesis, we performed multiple simulations on multiple GLIC systems with propofol occupying 0, 1, 2, 3, or 5 of the potential sites. We found that systems with symmetric ligand occupancy (0 or 5 bound propofols) showed similar channel conformation and hydration statuses. However, systems breaking the five-fold symmetry (1, 2, or 3 bound propofols) showed accelerated channel dehydration, increased conformational entropy of the pore-lining TM2 helix, and shifted tilting angles of the TM2 helix towards the closed-channel conformation. The trajectory of the force generated by propofol within each subunit is ellipsoidal with the primary force component tangential to the pore. Asymmetric ligand occupancy induced an unbalanced force around the channel, perturbed global stability, and facilitated conformational change. Our study suggests that asymmetry induced by ligand binding plays an important role in eliciting conformational changes related to protein function. Supported by NIH (R01GM066358, R01GM056257, R37GM049202, and T32GM075770) as well as the NSF via TeraGrid resources.