Module structure of interphotoreceptor retinoid-binding protein (IRBP) may provide bases for its complex role in the visual cycle – structure/function study of Xenopus IRBP

<p>Abstract</p> <p>Background</p> <p>Interphotoreceptor retinoid-binding protein's (IRBP) remarkable module structure may be critical to its role in mediating the transport of all-<it>trans and 11-cis </it>retinol, and 11-<it>cis </it>retinal between rods, cones, RPE and Müller cells during the visual cycle. We isolated cDNAs for <it>Xenopus </it>IRBP, and expressed and purified its individual modules, module combinations, and the full-length polypeptide. Binding of all-<it>trans </it>retinol, 11-cis retinal and 9-(9-anthroyloxy) stearic acid were characterized by fluorescence spectroscopy monitoring ligand-fluorescence enhancement, quenching of endogenous protein fluorescence, and energy transfer. Finally, the X-ray crystal structure of module-2 was used to predict the location of the ligand-binding sites, and compare their structures among modules using homology modeling.</p> <p>Results</p> <p>The full-length <it>Xenopus </it>IRBP cDNA codes for a polypeptide of 1,197 amino acid residues beginning with a signal peptide followed by four homologous modules each ~300 amino acid residues in length. Modules 1 and 3 are more closely related to each other than either is to modules 2 and 4. Modules 1 and 4 are most similar to the N- and C-terminal modules of the two module IRBP of teleosts. Our data are consistent with the model that vertebrate IRBPs arose through two genetic duplication events, but that the middle two modules were lost during the evolution of the ray finned fish. The sequence of the expressed full-length IRBP was confirmed by liquid chromatography-tandem mass spectrometry. The recombinant full-length <it>Xenopus </it>IRBP bound all-<it>trans </it>retinol and 11-<it>cis </it>retinaldehyde at 3 to 4 sites with <it>K</it>_<it>d</it>'s of 0.2 to 0.3 μM, and was active in protecting all-<it>trans </it>retinol from degradation. Module 2 showed selectivity for all-<it>trans </it>retinol over 11-cis retinaldehyde. The binding data are correlated to the results of docking of all-<it>trans</it>-retinol to the crystal structure of <it>Xenopus </it>module 2 suggesting two ligand-binding sites. However, homology modeling of modules 1, 3 and 4 indicate that both sites may not be available for binding of ligands in all four modules.</p> <p>Conclusion</p> <p>Although its four modules are homologous and each capable of supporting ligand-binding activity, structural differences between their ligand-binding domains, and interactions between the modules themselves will be critical to understanding IRBP's complex role in the visual cycle.</p