CommentaryComparative modeling of GABAA receptors: limits, insights, future developments
Section snippets
Sequence versus fold conservation and modeling at low sequence identity
Comparative modeling is based on the observation that in protein families, structure is more conserved than sequence (Russell et al., 1997). (The term “comparative modeling” is often used synonymously with the term “homology modeling.” Strictly speaking, homology modeling refers to modeling at assured homology. We prefer “comparative modeling” due to its more general definition [modeling at presumed homology]). Consequently, the unknown structure of a protein can be approximated “by comparison”
Regions of the GABAA receptor extracellular domain dissimilar from AChBP
Based on the family conservation patterns and results from the fold prediction server 3D-pssm Fischer et al., 1999, Kelley et al., 1999, Kelley et al., 2000, we estimate that in GABAA receptor subunits 60–75% of amino acid residues possess structural equivalents in the modeling template AChBP. This is shown for the GABAA receptor α1 subunit in Fig. 1 (in the line labeled GABα1 SO). Obviously, most variation will be found for beginnings and endings of long secondary structure motifs, lengths and
Local model quality in the ligand binding pockets
In our study we have investigated multiple alignment variants on the basis of the one shown in Fig. 2. They were submitted to the sequence-structure homology recognition server FUGUE (Shi et al., 2001) to be adjusted for best compatibility between AChBP structure and the sequences of individual subunits of GABAA receptors and to optimize insertion placements. Additional variants were generated based on data obtained from the fold prediction server 3D-pssm Fischer et al., 1999, Kelley et al.,
Defining the binding sites
Informed use of comparative models, even at low sequence identity, still can provide a wealth of insights. Given the high amount of conservation in the topography of the binding site among cys-loop receptors, conclusions can be drawn even from models with some degree of fuzziness. The high homology between the acetylcholine (ACh) binding site in nAChRs and AChBP formed the basis for modeling and docking studies of homo- and heteropentameric nAChRs that have led to the successful identification
Exploring different conformational states of pentameric ligand-gated ion channels
Any structural model of ligand-gated ion channels also raises questions concerning the allosteric state that is being modeled, as these receptors undergo appreciable conformational changes between basal (resting), activated and desensitized states (Chang and Weiss, 2002). The AChBP crystal structure most likely represents an agonist bound conformation, that could correspond to active or desensitized state conformations of the extracellular domain. An interesting model of a presumed resting
Conclusions
Rigorously validated model ensembles of the extracellular domain of GABAA receptors provide the possible 3D structure and local uncertainties of their ligand binding domains. The limited accuracy results from the low sequence identity between target and template and the differences between the soluble template and the membrane bound targets. However, rational mutagenesis experiments can be planned on the basis of present model structures, as overall topography is highly conserved (Brejc et al.,
Acknowledgements
The authors are grateful to Erich Grillitsch for assistance with Fig. 2, to Othmar Steinhauser for providing computational resources, to Daniel Rigden, Katherine Kantardjieff and Bernhard Rupp for helpful discussions. This work was supported by grant P15165 of the Austrian Science Fund.
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