Abstract

Microbial rhodopsins are integral membrane proteins that function as light-driven ion pumps or photoreceptors, playing a critical role in the phototactic and energy-harvesting mechanisms of various microorganisms. Many of these rhodopsins, particularly those from the *Hymenobacter* genus, are known to associate with carotenoid pigments, which can enhance light-harvesting efficiency and photoprotection. Understanding the structural dynamics and interaction between the rhodopsin and its associated carotenoid is a crucial initial step for investigating the protein's photochemical cycle. This study employed **long time-scale classical Molecular Dynamics (MD) simulations** to explore the structural stability and dynamic behavior of the **Hymenobacter psoromatis rhodopsin-carotenoid complex** embedded within a lipid bilayer. The primary objective was to sample the conformational space of the complex and characterize the nature of the rhodopsin-carotenoid binding pocket. Our simulations reveal a **tight and stable binding** of the carotenoid molecule to the rhodopsin, suggesting a highly conserved interaction motif. Specifically, the average distance between the closest atoms of the carotenoid and the protein was found to be exceptionally short, indicating a strong, non-covalent association. These structural insights provide a robust foundation for subsequent **quantum-classical (QM/MM) investigations** into the light-induced isomerization and proton-pumping mechanism, ultimately contributing to a deeper understanding of microbial photobiology and the design of novel optogenetic tools.