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Modelling the GABAA - receptor in the open and closed state
The GABAA receptor is a member of the Cys-loop family of ligand-gated ion channels. There are currently no high-resolution images of the GABAA receptor so the structure can only be inferred by homology modelling. In 2001, Brejc et al. crystallised acetylcholine binding protein (AChBP), a protein homologous to the extracellular domain of the Cys-loop family in the open state. This was followed by the publication of the nACh receptor structure in a closed state, obtained from electron microscopy data by Unwin (2005). From these structures, two models of the GABAA receptor (2α12β21γ2) were generated. The AChBP structure (pdb id: 1i9b) was used to produce an open-state model and the nACh receptor structure (pdb id: 2bg9) for a closed-state model. The human GABAA subunit sequences were aligned to the AChBP and nACh sequences using FUGUE (Shi et al., 2001), pairing the dominant binding subunits nACh α with GABAA β2. The GABA sequences were then thread over the homologous structures using MODELLER (Sali et al., 1993). The lowest energy models, where at least 92% of residues fell within allowed regions on a Ramachandran plot, were selected. The models show that the residues from the six GABA binding domains (A-F), identified using site-directed mutagenesis, photoaffinity labelling and the substituted cysteine accessibility method (Akabas, 2004), are located at the subunit interface. Apart from domains D and E, there are marked differences in the geometry of the GABA binding domains in the closed and open forms. In the latter, loop A is closer to the α-subunit, loop F contracts forming some secondary structural elements and loop B flexes towards the binding site. The most significant movement occurs at loop C, which moves 4.5Ǻ towards the α-subunit condensing the aromatic box formed by ligand binding residues α1 F65, β2Y97, β2Y157 and β2Y205. The closed model of the GABAA receptor also includes transmembrane structures. Channel-lining residues identified by Xu and Akabas (1996) project into the pore in this model. The model also identifies that α1K279 is located at the top of M2 close to α1D57, and β2 D146 is close to pre-M1 β2 K215. These residues are all thought to be involved in GABAA receptor gating (Kash et al. 2003; 2004). These models support previous data and also identify a number of potential residue movements that may prove critical to binding and receptor gating.
Akabas M.H. (2004) Int. Rev. Neurobiol. 62:1-43. |
