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Example sentences for: achbp
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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 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.
The calculated energies suggest a lower affinity of nicotine for alpha7-alpha7 than for alpha4-beta2, which is in agreement with experiments [ 3 ] . The ligands were also docked to the crystal structure of AChBP (the binding conformation was identical as with nAChRs), and the binding energies calculated.
These amino acids form a cluster in the proposed acetylcholine binding domain of AChBP similar to that proposed in our model.
We also docked HEPES to the receptors, since this ligand was found in the crystal structure of AChBP.
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