Long Time-Scale Classical MD Simulation of Hymenobacter psoromatis Rhodopsin with Carotenoid: An Initial Step for Photochemical Investigation

Abstract

Nowadays, only a few structures of rhodopsins bound with carotenoid were obtained and functionally characterized. Nevertheless, rhodopsins-carotenoids complexes are promising molecular systems for understanding the light-harvesting process in bacteria since such complexes show ability to absorb a significant part of solar energy coming to the Earth surface. The understanding of energy absorption and transfer mechanisms in the carotenoid-retinal complex of rhodopsin would provide significant progress in different areas of modern bioscience such as ecology, protein engineering, optogenetics, etc. Here we present a long (1 µs) molecular dynamical investigation of the structure of microbial rhodopsin from an Antarctic bacterium Hymenobacter psoromatis (strain PAMC26554) (HbR1) and zeaxanthin. The structure of rhodopsin was predicted with a new multi-modal foundation for molecular structure prediction Chai-1 and used for classical MD validation in a 10 × 10 × 12 nm box in a hydrated explicit lipid bilayer. Our simulations show tight binding of the carotenoid and rhodopsin with the average distance equal to 0.25 nm between the closest atoms of carotenoid and retinal.