Enhanced meta‐analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors

Abstract

The soluble acetylcholine binding protein (AChBP) is the default structural proxy for pentameric ligand-gated ion channels (LGICs). Unfortunately, it is difficult to recognize conformational signatures of LGIC agonism and antagonism within the large set of AChBP crystal structures in both apo and ligand-bound states, primarily because AChBP conformations in this set are nearly superimposable (root mean square deviation < 1.5 Å ). We have undertaken a systematic, alignment-free approach to elucidate conformational differences displayed by AChBP that cleanly differentiate apo/antagonist-bound from agonist-bound states. Our approach uses statistical inference based on both crystallographic states and conformations sampled during long molecular dynamics simulations to select important inter-C a distances and map their collective values onto functional states. We observe that binding of (nAChR) agonists to AChBP elicits clockwise rotation of the inner b-sheet with respect to the outer b-sheet, causing tilting of the cys-loop away from the five-fold axis, in a manner quite similar to that speculated for a-subunits of the heteromeric nAChR structure (Unwin, J Mol Biol 2005;346:967), making this motion potentially important in transmission of the gating signal to the transmembrane domain of a LGIC. The method is also successful at discriminating partial from full agonists and supports the hypothesis that a particularly controversial ligand, lobeline, is in fact an LGIC antagonist.

GABA Binding to an Insect GABA Receptor: A Molecular Dynamics and Mutagenesis Study

“…Such analyses also provide insight into the dynamic nature of protein-ligand interactions, a feature often not readily apparent from crystal structures. Many studies have used these techniques to probe the interactions of small ligands with their binding sites in the extracellular domain (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30), and simulations have also revealed information on the mechanism of peptide neurotoxin action and the role of cholesterol in nACh receptor function (52)(53)(54)(55). MD studies have also been used to probe the structural characteristics of the TMD, and as a means to elucidate the structural determinants governing channel opening, mostly in nACh receptors, and in the bacterial homologs ELIC and GLIC .…”

“…The availability of experimental structures and homology models has allowed the use of in silico methods to explore a range of Cys-loop receptor features, including ligand binding and conformational change at the extracellular domain (e.g., in AChBP (15)(16)(17), GABA C (18), nACh (19,20), and 5-HT 3 receptors (21,22)), and characterization of antidepressant and anesthetic binding sites (23)(24)(25)(26)(27)(28)(29)(30). Some of these data are supported by functional data: in the GABA C receptor, for example, MD simulations elucidated a key role for a loop D Arg stabilizing the carboxylate of GABA, and this role was confirmed using mutagenesis studies: when R104 is substituted with Ala or Glu an increase in GABA EC 50 >10,000-fold was observed (18).…”

Energetics and Mechanism of the Normal-to-Amyloidogenic Isomerization of β2-Microglobulin: On-the-Fly String Method Calculations

“…The residue pairs defining the twenty inter-C α distances were selected based on a statistical comparison of each pair of structures (normal and amyloidogenic), following the approach we recently developed for the acetylcholine binding protein. 18 These are (22,32); (11,32); (63,86); (86,92); (8,16); (32,88); (18,70); (11,63); (21,63); (27,86); (33,61); (31,39); (56,60); (18,42); (10,17); (18,94); (32,78); (17,86); (31,48); and (8,86). These are illustrated in Figure 2.…”

Minimal Structural Changes Determine Full and Partial Nicotinic Receptor Agonist Activity for Nicotine Analogues

“…The crystal structure of the ACh-binding protein (AChBP) from different species in the complex with several ligands, as well as derived homology models, have revealed the structural characteristics of the extracellular domain of nAChRs, as well as critical ligand-receptor interactions [12]. In addition, the recent description of the X-ray structure of a near-intact α4β2 nAChR bound to nicotine [13,14] has provided new insights regarding both the agonist binding site (the orthosteric site) and the structural requirements of its ligands.…”