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Example sentences for: achbp
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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.
The amino acids W89, R91 Y140, Y142 and Y152 of the 5HT 3 A R can be aligned with W53, Q55, L102, R104, and M114 of the AChBP (Figure 6).
R91, E106, F107, W183 and several residues adjacent to the M1 region have all been demonstrated to alter the action of 5-HT and/or m CPBG [ 20 21 25 26 ] . Within the crystal structure of the AChBP, homologous residues are located in the apparent binding site [ 24 ] . The effects of agonist on the 5-HT 3 R are mediated by their interaction with these binding site residues, resulting in stable receptor conformations, including the channel open state.
Low-energy conformations were found only in the absence of water molecule, and the calculated binding energies (Table 1- bottom) suggest that HEPES is a poor ligand for nAChRs, and AChBP, and was observed in the crystal structure because of its high concentration (100 mM) in the crystallization condition [ 6 ] .
The sequences of AChBP, and of the alpha3, alpha4, alpha7, beta2 and beta4 nAChR monomers were aligned using the ICM multiple sequence alignment algorithm that includes the following steps [ 16 10 ] : 1) pairwise alignment using Needleman and Wunsch algorithm modified to use zero end gap penalties (so called ZEGA) [ 15 16 ] . 2) evolutionary tree construction with a "neighbor-joining algorithm" to determine the order of alignment and calculate relative weights of sequences and profiles from the branch lengths [ 17 ] . 3) traverse the tree from top to bottom, aligning the closest sequences or profiles.
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