Structural evaluation of distant homology. A 3-D model of the ligand binding domain of the nicotinic acetylcholine receptor based on acetylcholinesterase: Consistency with experimental data

Acetylcholine is a ligand for both acetylcholinesterases and nicotinic acetylcholine receptors. Hence, at least some local sequence and structural similarities between the acetylcholinesterases and the receptors which recognize acetylcholine (ACh) might be expected. Peterson [2] produced an alignment of the ACh binding region between these two types of ACh-binding molecules, featuring a number of well conserved residues. The extent of this region of sequence similarity suggests the possible existence of a common ancenstral ACh binding module. To attempt to further validate Peterson's sequence alignment we have built a homology model of the ACh binding domain of the human neuromuscular nicotinic acetylcholine receptor based on the structure of acetylcholinesterase from Torpedo californica. Using this 3-D model we have examined the residues which were previously shown to interact with the endogenous ligand by various methods (mapping, site-directed mutagenesis). The consistency of such data with the model provides further support for a structural similarity and possibly a divergent evolutionary relationship between the ACh-binding domains of these two classes of proteins. Results suggest that this model may be able to contribute to an understanding of the structure and function of the ACh receptor. Using this case as an example, we propose that 3-dimensional computer modeling can be used as a tool to evaluate distant homologies when adequate experimental data (e.g., site-directed mutagenesis) is available.