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Investigating the Putative Binding-mode of GABA and Diazepam within GABA(A) Receptor Using Molecular Modeling.

Ci S, Ren T, Su Z

National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100080, P.R. China, trren@home.ipe.ac.cn.

The three-dimensional structure of the GABA(A) receptor that included the ligand/agonist binding site was constructed and validated by using molecular modeling technology. Moreover, the putative binding-mode of GABA and diazepam with GABA(A) receptor were investigated by means of docking studies. Based on an rmsd-tolerance of 1.0 A, the docking of GABA to alpha1/beta2 interface resulted in three multi-member conformational clusters and model 2 was supported by homologous sequence alignment data and experimental evidence. On the other hand, the docking of diazepam to alpha1/gamma2 interface revealed five multi-member conformational clusters in the binding site and model 1 seemed to represent the correct orientation of diazepam in the binding site.

Published 6 September 2007 in Protein J.
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