Symmetry-Adapted Markov State Models of Closing, Opening, and Desensitizing in 7 nicotinic acetylcholine receptors

α7 nicotinic acetylcholine receptors (nAChRs) are homopentameric ligand-gated ion channels gated by acetylcholine. These receptors play crucial roles in controlling electrical signaling within the nervous system by facilitating the passage of cations across the membrane. Recent studies have resolved and functionally annotated closed, open, and desensitized states of α7 nAChRs, providing insight into ion permeation and lipid modulation. However, the process by which α7 nAChRs transition between states remains unclear. To understand gating and lipid modulation, we generated two ensembles of molecular dynamics simulations of the apo form of α7 nAChRs, with or without cholesterol. Using symmetry-adapted Markov state modeling, we developed a five-state gating model. Free energies recapitulated functional behavior, with the closed state dominating in the absence of agonists. Notably, the transition rate from open to a non-conductive intermediate (flipped) state corresponded to experimentally measured open durations around 0.1 ms. The introduction of cholesterol relatively stabilized the desensitized state and reduced barriers between desensitized and open states. These results establish plausible asymmetric transition pathways between functionally important states, they define lipid modulation effects in the α7 nAChR conformational cycle, and provide an ensemble of structural models that could be utilized for guiding rational design strategies to develop lipidic pharmaceuticals targeting these receptors. ### Competing Interest Statement The authors have declared no competing interest.