Rhodopsin Transient Complexes Investigated by Systems Biology Approaches

Abstract

The fast kinetics characterizing the phototransduction cascade in virtually any species require that rhodopsin (Rh) form transient molecular complexes with a multitude of other proteins. Isolating such transient interactions in vitro and in vivo is a challenging task, although understanding their dynamics is essential to fully understand Rh function. Here, an established bottom-up systems biology approach is summarized, which links individual biomolecular processes to the whole-cell response, namely, the light-dependent suppression of the photoreceptor dark current. The known biochemical interactions occurring in the phototransduction cascade are integrated into a comprehensive computational model that can be numerically simulated, making it possible to: (a) virtually follow the time course of transient complexes formed by Rh with other molecules, including the cognate G protein transducin (Gt), rhodopsin kinase (RK), and arrestin (Arr), and (b) focus on specific receptor states, including multiple phosphorylations and activity of the chromophore-free receptor (opsin, Ops). Successful predictions of retinal disease-associated states, such as those related to vitamin A deficiency and Leber congenital amaurosis, have been obtained with the methodology presented herein.

Protein and Signaling Networks in Vertebrate Photoreceptor Cells

“…Dark rhodopsin-transducin binding occurs with submicromolar affinity and is characterized by very fast association and dissociation rates in a “dynamic scaffolding” frame, where concerted diffusion/binding phenomena give rise to a dynamic hopping of transducin on rhodopsin supramolecular assemblies (Dell’Orco and Koch, 2011 ). The transient precoupling step was integrated into the framework of phototransduction models of both amphibian and murine rods, and was found to be compatible with the overall cascade kinetics (Invergo et al, 2014 ; Dell’Orco, 2015 ). The physiological presence of rhodopsin-transducin transient complexes has been somewhat questioned and debated (Schöneberg et al, 2014 , 2015 ; Dell’Orco and Koch, 2015 ), however it appears now quite clear that it may have deep implications for the capability of rods to detect single photons (Cangiano and Dell’Orco, 2013 ; Dell’Orco, 2013 ), and seems to be an essential mechanistic step in the recently emerged picture of rhodopsin tracks observed by cryoelectron tomography, in order to create the “kinetic traps”: owing to the frequent, rapid formation and breakup of precomplexes, transducin molecules could scan a rhodopsin track by discrete hopping events, resulting in an activation rate that, in the single-photon regime, would be determined by the number of the preassembled transducin molecules per track rather than the photoactivated rhodopsin lifetime.…”