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

IF 1.1 Q4 CELL BIOLOGY
A. Kh. Taldaev, D. A. Fedotov, I. S. Okhrimenko
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引用次数: 0

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.

类胡萝卜素在长时间尺度上的经典MD模拟:光化学研究的第一步
目前,仅获得了几种与类胡萝卜素结合的视紫红质结构并进行了功能表征。然而,视紫红质-类胡萝卜素复合物是一种很有前途的分子系统,可以用来理解细菌的光收集过程,因为这种复合物显示出吸收大部分到达地球表面的太阳能的能力。了解视紫红质类胡萝卜素-视网膜复合物的能量吸收和传递机制,将为生态学、蛋白质工程、光遗传学等现代生物科学的不同领域提供重要的研究进展。在这里,我们对南极细菌psoromatis膜杆菌(菌株PAMC26554) (HbR1)的微生物紫红质结构和玉米黄质进行了长时间(1µs)的分子动力学研究。利用新的多模态分子结构预测基础Chai-1预测了紫红质的结构,并在水合外显脂质双分子层的10 × 10 × 12 nm盒子中进行了经典的MD验证。我们的模拟表明,类胡萝卜素和视紫红质紧密结合,最接近的类胡萝卜素原子和视网膜之间的平均距离为0.25 nm。
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来源期刊
CiteScore
1.40
自引率
0.00%
发文量
28
期刊介绍: Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology   is an international peer reviewed journal that publishes original articles on physical, chemical, and molecular mechanisms that underlie basic properties of biological membranes and mediate membrane-related cellular functions. The primary topics of the journal are membrane structure, mechanisms of membrane transport, bioenergetics and photobiology, intracellular signaling as well as membrane aspects of cell biology, immunology, and medicine. The journal is multidisciplinary and gives preference to those articles that employ a variety of experimental approaches, basically in biophysics but also in biochemistry, cytology, and molecular biology. The journal publishes articles that strive for unveiling membrane and cellular functions through innovative theoretical models and computer simulations.
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