A structural and functional bioinformatics study of QTY-designed retinylidene proteins

Retinylidene proteins are retinal-binding light-sensitive proteins found in organisms ranging from microbes to human. Microbial opsins have been utilized in optogenetics, while animal opsins are essential for vision and light-dependent metabolic functions. However, retinylidene proteins have hydrophobic transmembrane (TM) domains, which makes them challenging to study. In this structural and functional bioinformatics study, I use the QTY (glutamine, threonine, tyrosine) code to design water-soluble QTY analogues of retinylidene proteins, including nine human and three microbial opsins. I provide superpositions of the AlphaFold3-predicted hydrophobic native proteins and their water-soluble QTY analogues, and experimentally determined structures when available. I also provide a comparison of surface hydrophobicity of the variants. Despite significant changes to the protein sequence (35.53-50.24% in the TM domain), protein characteristics and structures are well preserved. Furthermore, I run molecular dynamics (MD) simulations of native and QTY-designed OPN2 (rhodopsin) and analyze their response to the isomerization of 11-<i>cis</i>-retinal to all-<i>trans</i>-retinal. The results show that the QTY analogue has similar functional behavior to the native protein. The findings of this study indicate that the QTY code can be used as a robust tool to design water-soluble retinylidene proteins. These have potential applications in protein studies, therapeutic treatments, and bioengineering.