Conformational signatures of native ligand and pharmacochaperone binding in rhodopsin

Rhodopsin misfolding underlies rhodopsin-linked retinitis pigmentosa, and small-molecule pharmacochaperones represent a promising therapeutic strategy. However, the mechanisms by which these compounds interact with and stabilize rhodopsin remain poorly understood. Here, we combine backbone amide hydrogen-deuterium exchange mass spectrometry (amide HDX-MS), histidine-specific HDX (His-HDX), protein structure network (PSN) analysis, molecular docking, and functional spectroscopy to define ligand-induced conformational signatures in this receptor elicited by three non-retinoid small molecules, quercetin, myricetin, and the chromenone CR5, and to compare them with those of the native chromophore 11-cis-retinal. Binding of 11-cis-retinal to ligand-free opsin establishes a benchmark orthosteric conformational signature, characterized by strong backbone HDX protection across TM4-TM7 and adjacent loops, suppression of EX1-like hydrogen-deuterium exchange kinetics at the N-terminal ends of TM1 and TM4, and reorganization of PSN hubs that stabilizes an inactive-state residue interaction network. All three non-retinoid ligands generate HDX footprints that closely track this retinal-induced pattern within the chromophore pocket, consistent with direct orthosteric engagement, but they confer weaker and ligand-specific stabilization. Among them, quercetin most closely reproduces the retinal-like backbone protection and His-HDX microenvironment changes, whereas myricetin and CR5 only partially recapitulate retinal-induced stabilization and redistribute conformational flexibility toward TM1 and intradiscal regions, without fully suppressing EX1-like gating. In addition, all three compounds induce weak cytoplasmic allosteric effects in retinal-bound rhodopsin, indicating secondary interactions in addition to a primary orthosteric mechanism. Together, these results provide the first residue-level experimental framework for understanding the differential pharmacochaperoning capacity of non-retinoid ligands and highlight key conformational principles for future optimization of opsin stabilizers.