On the spatial disposition of the fifth transmembrane helix and the structural integrity of the transmembrane binding site in the opioid and ORL1 G protein-coupled receptor family
Topham, C.M.; Moulédous, L.; Meunier, J.C.
Protein Engineering 13(7): 477-490
ISSN/ISBN: 0269-2139 PMID: 10906343 DOI: 10.1093/protein/13.7.477
Evidence from statistical cluster analyses of a multiple sequence alignment of G protein-coupled receptor seven-helix folds supports the existence of structurally conserved transmembrane (TM) ligand binding sites in the opioid/opioid receptor-like (ORL1) and amine receptor families. Based on the expectation that functionally conserved regions in homologous proteins will display locally higher levels of sequence identity compared with global sequence similarities that pertain to the overall fold, this approach may have wider applications in functional genomics to annotate sequence data. Binding sites in models of the kappa-opioid receptor seven-helix bundle built from the rhodopsin templates of Baldwin et al. (1997) [J. Mol. Biol., 272, 144-164] and Herzyk and Hubbard (1998) [J. Mol. Biol., 281, 742-751] are compared. The Herzyk and Hubbard template is found to be in better accord with experimental studies of amine, opioid and rhodopsin receptors owing to the reduced physical separation of the extracellular parts of TM helices V and VI and differences in the rotational orientation of the N-terminal of helix V that reveal side chain accessibilities in the Baldwin et al. structure to be out of phase with relative alkylation rates of engineered cysteine residues in the TM binding site of the alpha(2A)-adrenergic receptor. TM helix V in the Baldwin et al. template has been remodelled with a different proline kink to satisfy experimental constraints. A recent proposal that rotation of helix V is associated with receptor activation is critically discussed.