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Example sentences for: achbp
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These amino acids form a cluster in the proposed acetylcholine binding domain of AChBP similar to that proposed in our model.
The AChBP displays a large amount of homology to the amino terminal of LGIC receptors and thus may be similar in structure [ 20 24 ] . The crystal structure of this protein reveals a loose 3 residue turn incorporating the conserved glycine residue [ 24 ] . Homologous residues in other LGIC subunits have also been identified and are shown in Figure 1. The residues identified in this study as altering binding affinity of 5-HT 3 R ligands would also be present on the same surface if this structure is present in the 5-HT 3 R. While Y140 lies somewhat outside the region identified by Chiara in the nAChR (homologous to γN107), γL109 and γL119 are homologous to Y142 and Y152 of the 5-HT 3AS R. The ability of lerisetron to interact with both Y142 and Y152 also supports the hypothesis that these two amino acids are present in a loop structure since the eight intervening residues would position Y142 and Y152 too far apart to permit them both to interact with a single ligand even if they were interacting with functional groups on opposite ends of the molecule.
This binding site coincides with that of AChBP, and is in agreement with photo-affinity labeling and mutagenesis study [ 6 11 ] . The ligand makes Van der Waals contact with Trp182, Tyr230 and Cys225-226 of alpha4, and Trp82, Leu146 and Phe144 of beta2 (Figure 3- Top).
For each nAChR dimer, two monomer sequences were threaded onto two consecutive subunits of the AChBP crystal structure, based on the multiple sequence alignment, and the energy of the system was locally minimized by the ICM method [ 10 18 ] . The orientation of all polar hydrogens was systematically optimized through conformational space search combined with local minimization.
In the center of this region is a critical glycine residue that is thought to play a role in establishing a hairpin loop [ 12 ] . Recent x-ray crystallographic data obtained from an ACh binding protein (AChBP) shows a loop structure in this region resulting from a 3 residue turn containing a glycine homologous to G147 of the 5-HT 3 R. On either side of this putative turn region are residues that have been identified as important to receptor binding [ 12 13 14 15 16 17 18 ] . The formation of this loop structure brings amino acids on either side of glycine into close proximity and may form a binding pocket that will accommodate one or more functional groups.
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