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

Abstract

Nicotinic AChRs (nAChRs) represent a paradigm for ligand-gated ion channels. Despite intensive studies over many years, our understanding of the mechanisms of activation and inhibition for nAChRs is still incomplete. Here, we present molecular dynamics (MD) simulations of the ␣7 nAChR ligand-binding domain, both in apo form and in ␣-Cobratoxin-bound form, starting from the respective homology models built on crystal structures of the acetylcholine-binding protein. The toxin-bound form was relatively stable, and its structure was validated by calculating mutational effects on the toxin-binding affinity. However, in the apo form, one subunit spontaneously moved away from the conformation of the other four subunits. This motion resembles what has been proposed for leading to channel opening. At the top, the C loop and the adjacent ␤7-␤8 loop swing downward and inward, whereas at the bottom, the F loop and the C terminus of ␤10 swing in the opposite direction. These swings appear to tilt the whole subunit clockwise. The resulting changes in solvent accessibility show strong correlation with experimental results by the substituted cysteine accessibility method upon addition of acetylcholine. Our MD simulation results suggest a mechanistic model in which the apo form, although predominantly sampling the ''closed'' state, can make excursions into the ''open'' state. The open state has high affinity for agonists, leading to channel activation, whereas the closed state upon distortion has high affinity for antagonists, leading to inhibition.allostery ͉ spontaneous opening ͉ ligand-gated ion channel ͉ ligand binding N icotinic AChRs (nAChRs) are a well studied prototype for ligand-gated ion channels (1-19). nAChRs are pentamers consisting of either homo or hetero subunits. The N-terminal extracellular regions of the subunits make up the ligand-binding domain (LBD), with two or five binding sites in hetero and homo pentamers, respectively. The central regions form the transmembrane domain (TMD), which is an ion channel selective for cations such as Na ϩ , K ϩ , and Ca 2ϩ [supporting information (SI) Fig. S1]. A central issue is the mechanisms of channel activation by agonists and inhibition by antagonists. How is agonist/ antagonist binding transmitted to trigger channel opening/ closing? What are the necessary conformational changes? Experimental and computational studies together have begun to provide mechanistic insights at the atomic level. Here, we present a molecular dynamics (MD) simulation study of the ␣7 nAChR LBD (consisting of five ␣-type subunits), both in apo form and in ␣-Cobratoxin-bound form. Our simulation results are in broad agreement with a wealth of experimental data. Combining the present work with experimental data and previous computational results, we propose a mechanistic model in which the apo form, although predominantly sampling the ''closed'' state, can make excursions into the ''open'' state. Details of the conformational change leading to channel activation/inhibition are presented.A number ...

Conformational heterogeneity of the M2 proton channel and a structural model for channel activation

“…Importantly, in the population that putatively becomes favored at low pH, the Trp-41 indole rings are oriented to open the channel pore. The shift in population by the binding of a ligand, a proton in the present case, is similar to what is suggested for a ligand-gated ion channel (38).…”

A prokaryotic perspective on pentameric ligand-gated ion channel structure

“…A similar overall conformational change in the LBD as found upon comparison of the ELIC and GLIC structures was found in molecular dynamic simulations of a homology model of the human α7 LBD [164] . Remarkably this change is not observed in the transition from the unoccupied to the ligand-bound AChBP, which stays relatively rigid except for the movements of the C-loop.…”

“…An alternative model is based on accessibility studies and electrophysiological recordings and denies any rotation of the helices [82] . This model proposes a tilt of the pore forming helices away from the channel axis in the intracellular end of the channel [68,164] , which removes the constriction at the intracellular end of the pore.…”

A gating mechanism of pentameric ligand-gated ion channels

“…Computational studies of pLGICs based on Normal Mode analysis (22,23) and Molecular Dynamics (24,33) have demonstrated that global twisting is encoded in the structural topology of these ion channels and have suggested a role for this quaternary change in the gating process. These findings were refined by the structural studies at high resolution of GLIC, ELIC, and GluCl, which demonstrated that, in addition to quaternary twisting, substantial tertiary changes in the TM domain determine the opening/closing of the ion pore (14)(15)(16)18).…”