Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors

Abstract

The initial coupling between ligand binding and channel gating in the human a7 nicotinic acetylcholine receptor (nAChR) has been investigated with targeted molecular dynamics (TMD) simulation. During the simulation, eight residues at the tip of the C-loop in two alternating subunits were forced to move toward a ligand-bound conformation as captured in the crystallographic structure of acetylcholine binding protein (AChBP) in complex with carbamoylcholine. Comparison of apo-and ligand-bound AChBP structures shows only minor rearrangements distal from the ligandbinding site. In contrast, comparison of apo and TMD simulation structures of the nAChR reveals significant changes toward the bottom of the ligand-binding domain. These structural rearrangements are subsequently translated to the pore domain, leading to a partly open channel within 4 ns of TMD simulation. Furthermore, we confirmed that two highly conserved residue pairs, one located near the ligand-binding pocket (Lys145 and Tyr188), and the other located toward the bottom of the ligand-binding domain (Arg206 and Glu45), are likely to play important roles in coupling agonist binding to channel gating. Overall, our simulations suggest that gating movements of the a7 receptor may involve relatively small structural changes within the ligand-binding domain, implying that the gating transition is energy-efficient and can be easily modulated by agonist binding/unbinding.

Spontaneous conformational change and toxin binding in α7 acetylcholine receptor: Insight into channel activation and inhibition

“…The global and local conformational change observed in one of the subunits is consistent with previous targeted MD simulations and normal mode analyses (17,18). That these conformational changes correspond to channel opening is supported by SCAM experiments upon agonist binding (10,19).…”

“…The opposite swings of the C and F loops are reminiscent of the motions seen in the targeted MD simulations of McCammon and coworkers (17). Note that in our simulations, the opposite swings occurred spontaneously, whereas in the study of McCammon and coworkers (17), the motions were triggered by pulling the C loop from the up to the down position, which was supposed to mimic agonist binding. In the cyan subunit, the C loop also moved toward the down position, but the rest of the molecule did not experience additional distortion, leading to the intermediate rmsd shown in Fig.…”

“…The toxin-bound form is found to be relatively stable, and the structure of the LBD-toxin complex is validated by comparing calculated mutational effects on the binding affinity against experimental data (8). In the apo form, one subunit spontaneously moves away from the ''closed'' conformation of the other subunits, with motions resembling those obtained in targeted MD simulations (17). We propose that this subunit has undergone a transition from the closed to the open conformation, whereas the other four subunits remain in the closed conformation.…”

“…allostery ͉ spontaneous opening ͉ ligand-gated ion channel ͉ ligand binding N icotinic AChRs (nAChRs) are a well studied prototype for ligand-gated ion channels (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). nAChRs are pentamers consisting of either homo or hetero subunits.…”

Myasthenic syndrome AChRα C-loop mutant disrupts initiation of channel gating

“…Subsequent studies, however, attained this goal by exploring energetic coupling among residues within or between subunits by combined mutagenesis studies, single-channel recordings, and thermodynamic mutant cycle analyses (20)(21)(22)(23)(24). These studies revealed that activation of the receptor begins by transition of the C-loop of each α subunit from an opened-up to a closed-in conformation (24)(25)(26); this leads to displacement of β-strand 10, which is contiguous with the pre-M1 domain, and results in conformational changes of the β1-β2 linker and the Cys-loop (Figure 1). Both the β1-β2 linker and the Cys-loop energetically couple with residues in the M2-M3 linker and in the course of channel opening displace the M2 helix away from the center of pore (21,23,27).…”