Structure of the Pentameric Ligand-Gated Ion Channel GLIC Bound with Anesthetic Ketamine

Abstract

SUMMARY Pentameric ligand-gated ion channels (pLGICs) are targets of general anesthetics, but a structural understanding of anesthetic action on pLGICs remains elusive. GLIC, a prokaryotic pLGIC, can be inhibited by anesthetics, including ketamine. The ketamine concentration leading to half-maximal inhibition on GLIC (58 µM) is comparable to that on neuronal nicotinic acetylcholine receptors. A 2.99-Å resolution X-ray structure of GLIC bound with ketamine revealed ketamine binding to an inter-subunit cavity that partially overlaps with the homologous antagonist-binding site in pLGICs. The functional relevance of the identified ketamine site was highlighted by profound changes in GLIC activation upon cysteine substitution of the cavity-lining residue N152. The relevance is also evidenced by changes in ketamine inhibition upon the subsequent chemical labeling of N152C. The results provide novel structural insight into the molecular recognition of ketamine and are valuable for understanding the actions of anesthetics and other allosteric modulators on pLGICs.

Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine

“…6C) (59), ketamine (pink spheres, Fig. 6C) (57), and acetate (firebrick spheres, Fig. 6C) (58) were already mentioned in the previous paragraphs.…”

“…6A) (54). This site corresponds to the ketamine binding site reported in the GLIC (57), where ketamine also binds just below the orthosteric agonist binding site and is involved in inhibition of GLIC (pink spheres, Fig. 6C).…”

Comparing crystal structures of Ca2+‐ATPase in the presence of different lipids

“…Both arginine and lysine residues are frequently found at membrane-interface regions, where they act as 'snorkeling' residues, pointing their positively charged side chain moiety towards the negative phospholipid head groups [3,29]. Correspondingly, arginine and lysine residues have been seen to coordinate lipid head groups on several occasions [30][31][32]. The advantage of mediating lipid interaction by such positively charged 'snorkeling' side chains, as opposed to, for example, a coordinated cation, is structural flexibility; flexible arrangements between both arginine and lysine side chains can easily accommodate different types of head groups, as well as fluctuations in the position of an interacting lipid, thereby allowing for a continuous and mutually adaptive cross-talk between the protein and the lipid bilayer, as also seen in MD simulations [3].…”

International Union of Basic and Clinical Pharmacology. XC. Multisite Pharmacology: Recommendations for the Nomenclature of Receptor Allosterism and Allosteric Ligands

“…This classic structural paradigm is also shared by other key pLGICs, such as the GABA A , glycine, and 5-HT 3 receptors. Numerous studies have established that the orthosteric sites on these receptors are located in the extracellular regions of subunit interfaces, at about 60 Å from the pore-forming transmembrane 2 (TM2) regions of each protomer (Changeux, 2013b); importantly, this has been directly confirmed through X-ray structural studies on related prokaryotic pentameric LGICs (Hibbs and Gouaux, 2011;Corringer et al, 2012;Pan et al, 2012).…”