Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance

For many species, vision is one of the most important sensory modalities for mediating essential tasks that include navigation, predation and foraging, predator avoidance, and numerous social behaviors. The vertebrate visual process begins when photons of the light interact with rod and cone photoreceptors that are present in the neural retina. Vertebrate visual photopigments are housed within these photoreceptor cells and are sensitive to a wide range of wavelengths that peak within the light spectrum, the latter of which is a function of the type of chromophore used and how it interacts with specific amino acid residues found within the opsin protein sequence. Minor differences in the amino acid sequences of the opsins are known to lead to large differences in the spectral peak of absorbance (i.e. the λmax value). In our prior studies, we developed a new approach that combined homology modeling and molecular dynamics simulations to gather structural information associated with chromophore conformation, then used it to generate statistical models for the accurate prediction of λmax values for photopigments derived from Rh1 and Rh2 amino acid sequences. In the present study, we test our novel approach to predict the λmax of phylogenetically distant Sws2 cone opsins. To build a model that can predict the λmax using our approach presented in our prior studies, we selected a spectrally-diverse set of 11 teleost Sws2 photopigments for which both amino acid sequence information and experimentally measured λmax values are known. The final first-order regression model, consisting of three terms associated with chromophore conformation, was sufficient to predict the λmax of Sws2 photopigments with high accuracy. This study further highlights the breadth of our approach in reliably predicting λmax values of Sws2 cone photopigments, evolutionary-more distant from template bovine RH1, and provided mechanistic insights into the role of known spectral tuning sites.Author summary: In vertebrates, color vision depends on the complement of cone visual photopigments that have different spectral peaks of absorbance (λmax) within the cone population. Together, the type of chromophore and the amino acid sequence of the opsin protein directly affect the λmax value. To understand this relationship further at a structural level, we previously developed a new molecular modeling approach to study Rh1 and Rh2 opsin classes by combining homology modeling, molecular dynamics simulations to extract structural parameters of chromophore conformations and statistical modeling. Here, we used this novel modeling approach to accurately predict the λmax values for teleost Sws2 photopigments. Such a genome-to-phenome approach for predicting visual pigment function will be of great interest to evolutionary biologists, vision scientists, and molecular modelers, to better understand the diversity and mechanisms of sensory function. Moreover, it will pave the way for novel strategies to forward engineer visual pigments suitable for optogenetics applications.