Ananchenko, Anna2025-04-222025-04-222025-04-22http://hdl.handle.net/10393/50359https://doi.org/10.20381/ruor-31034Ligand-gated ion channels (LGICs) are a diverse family of membrane proteins which play a key role in neuronal communication. The neuronal lipid membrane in which LGICs are embedded is a complex and dynamic environment which, over decades of LGIC research, has been shown to influence the function of these proteins. The specific lipid requirements and functional effects of membrane lipids differ by LGIC type. The presence of polyunsaturated fatty acids (PUFAs) modulates the pH response of acid-sensing ion channels (ASICs), and in the case of subtype ASIC3, can even activate the channels at physiological pH. Another type of LGIC, the nicotinic acetylcholine receptor (nAChR), requires the presence of anionic lipids and/or cholesterol for function. It has been proposed that lipids exert their function on LGICs through direct interactions at lipid binding sites. To date, however, these binding sites are poorly described, and their existence remains uncertain. High resolution cryo-EM structures of ASICs and nAChRs have been solved in recent years showing density attributed to bound lipids. Using multiscale molecular dynamics (MD simulations), I embed high-resolution structures of ASIC and the nAChR in membrane patches of interest to observe the dynamics of specific lipid interactions with these channels. My simulations suggest prolonged, direct interactions of functionally relevant lipids with the transmembrane domains (TMDs) of ASICs and nAChRs. Key arginine residues at the outer leaflet region of ASIC TMDs coordinate high-occupancy PUFA interactions which can be disrupted by in-silico mutagenesis. Similarly, the activity-promoting lipids phosphatidic acid (PA) and cholesterol bind to specific sites with longer duration than the lipid phosphatidylcholine (PC), which does not promote activity. The relative binding free energy of PA and PC was calculated using free energy perturbation at a conserved nAChR inner leaflet site, estimating a 1.5 kcal/mol difference between the two lipids, revealing slight preferential binding for PA. Together these findings suggest that activity-promoting lipids species bind to specific lipid binding sites which higher affinity than bulk membrane lipids, and these interactions could stabilize active or activatable states of LGICs.enBiochemistryBiophysicsProtein-lipid InteractionsLigand-gated Ion ChannelsMolecular Dynamics SimulationsThesis