Genetic characterization of the visual pigments of the red-eared turtle (Trachemys scripta elegans) and computational predictions of the spectral sensitivity

Abstract

The visual processing of vertebrates initiates in the retina upon the absorbance of photons by the photoreceptors. These neurons contain the photopigments that are formed by a membrane protein, opsin or rhodopsin, covalently bound to a chromophore. The peak spectral sensitivity (λ_max) of the photopigment is determined by the protein structure and the type of chromophore associated, 11-cis-retinal (A₁-based chromophore) or 3,4-dehydroretinal (A₂-based chromophore). The red-eared turtle, Trachemys scripta elegans, has five A₂-based photopigments, SWS1, SWS2, RH1, RH2, and LWS, with known λ_max at 372, 458, 518, 518, and 617 nm, respectively. We took advantage of this valuable model to investigate the applicability of computational modeling to estimate the λ_max of A₂-based opsins. First, we sequenced the five opsin genes expressed in the retina of T. s. elegans and estimated the opsins λ_max based on known spectral tuning sites. The predictions were consistent with the values described in the literature: 373, 457, 518, 518, and 617 nm, for the SWS1, SWS2, RH1, RH2, and LWS, respectively. Then, we calculated the λ_max using Comparative Modeling for the RH1, RH2, SWS1, and SWS2 opsins and using Threading Modeling for the LWS opsin. The absorption spectrum was analyzed using semiempirical Quantum Mechanical simulations, according to the TD-DFT method, applying the functional B3LYP and 6–31 G basis set. For each model, molecular docking was carried out to find the best positioning of the chromophore. The estimated λ_max of the SWS1, RH1, and RH2 were consistent with known peaks (380, 524, and 520 nm, respectively), while the opsins SWS2 and LWS had considerable shifts compared to known values (478 and 636 nm, respectively). Although the calculated λ_max of the cone opsins had some inconsistencies, the in silico analyses revealed promising results and opened a new methodologic approach for further investigations of vertebrate spectral sensitivity.