Bertalan Éva, Bondar Ana-Nicoleta
Physikzentrum, RWTH Aachen University, Aachen, Germany.
Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany.
Front Chem. 2023 Jan 13;10:1075648. doi: 10.3389/fchem.2022.1075648. eCollection 2022.
Microbial rhodopsins are membrane proteins that use the energy absorbed by the covalently bound retinal chromophore to initiate reaction cycles resulting in ion transport or signal transduction. Thousands of distinct microbial rhodopsins are known and, for many rhodopsins, three-dimensional structures have been solved with structural biology, including as entire sets of structures solved with serial femtosecond crystallography. This sets the stage for comprehensive studies of large datasets of static protein structures to dissect structural elements that provide functional specificity to the various microbial rhodopsins. A challenge, however, is how to analyze efficiently intra-molecular interactions based on large datasets of static protein structures. Our perspective discusses the usefulness of graph-based approaches to dissect structural movies of microbial rhodopsins solved with time-resolved crystallography.
微生物视紫红质是膜蛋白，它们利用与共价结合的视黄醛发色团吸收的能量来启动反应循环，从而导致离子运输或信号转导。已知有成千上万种不同的微生物视紫红质，并且对于许多视紫红质来说，其三维结构已通过结构生物学解析出来，包括通过串行飞秒晶体学解析出的完整结构集。这为全面研究静态蛋白质结构的大型数据集奠定了基础，以便剖析为各种微生物视紫红质提供功能特异性的结构元件。然而，一个挑战是如何基于静态蛋白质结构的大型数据集有效地分析分子内相互作用。我们的观点讨论了基于图的方法在剖析通过时间分辨晶体学解析出的微生物视紫红质结构动态过程方面的有用性。
