The soluble acetylcholine binding protein (AChBP) has served for many years as a structural proxy for members of the superfamily of pentameric ligand-gated ion channels (LGICs), which are integral to many biological functions across an array of species. Unfortunately, it has so far proven difficult to extract detailed conformational signatures unique to agonism and antagonism of LGIC's from the large set of AChBP crystal structures in both apo and ligand-bound states, primarily because AChBP conformations are fairly invariant across this set (mean RMSD < 1.5 Å), resulting in alignment artifacts that make comparing structures for the purposes of identifying conformational changes problematic. To address this, we have undertaken a systematic approach to elucidate conformational signatures displayed by AChBP that differentiate apo/antagonist-bound from agonist-bound states. Our method side-steps alignment artifacts by using statistical inference based on inter-α-carbon distances from both crystallographic states and conformations sampled during long molecular dynamics (MD) simulations. Using this method in conjunction with MD simulation of an agonist-bound structure, we observed that binding of agonists of the nicotinic acetylcholine receptor (nAChR) to AChBP elicits clockwise rotation of the inner β-sheet with respect to the outer β-sheet, causing tilting of the cys-loop. This motion is similar to that suggested by comparing conformations of α and non-α subunits in the heteromeric nAChR, and is potentially important in transmission of the gating signal to the transmembrane domain of a LGIC (Unwin, J. Mol. Biol. 2005;346:967-989). The method is also successful in discriminating partial from full nAChR-agonists, and supports the hypothesis that a particularly controversial ligand, lobeline, is in fact an LGIC antagonist.
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