ArticleQRB discovery2025
A structural and functional bioinformatics study of QTY-designed retinylidene proteins.
Article in QRB discovery, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Abstract
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-
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