Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Berlin, Germany.
University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN.
Photochem Photobiol. 2017 Nov;93(6):1336-1344. doi: 10.1111/php.12790. Epub 2017 Jul 25.
Channel and pump rhodopsins use energy from light absorbed by a covalently bound retinal chromophore to transport ions across membranes of microbial cells. Ion transfer steps, including proton transfer, can couple to changes in protein conformational dynamics and water positions. Although general principles of how microbial rhodopsins function are largely understood, key issues pertaining to reaction mechanisms remain unclear. In this review, we compare the protonation-coupled dynamics of pump and channelrhodopsins, highlighting the roles that water dynamics, protein electrostatics and protein flexibility can have in ion transport mechanisms. We discuss observations supporting important functional roles of inter- and intra-helical carboxylate/hydroxyl hydrogen-bonding motifs. As specific examples, we use the proton pump bacteriorhodopsin, the sodium pump KR2, channelrhodopsins and Anabaena sensory rhodopsin. We outline the usefulness of theoretic biophysics approaches to the study of retinal proteins, challenges in studying the hydrogen-bond dynamics of rhodopsin active sites, and implications for conformational coupling in membrane transporters.
通道和泵视紫红质利用共价结合的视黄醛色素吸收的光能将离子跨微生物细胞的膜运输。离子转移步骤，包括质子转移，可以与蛋白质构象动力学和水位置的变化偶联。尽管微生物视紫红质的功能的一般原理在很大程度上被理解，但与反应机制相关的关键问题仍然不清楚。在这篇综述中，我们比较了泵和通道视紫红质的质子偶联动力学，强调了水动力学、蛋白质静电和蛋白质柔韧性在离子传输机制中可能具有的作用。我们讨论了支持跨和内螺旋羧酸盐/羟基氢键模体重要功能作用的观察结果。作为具体的例子，我们使用质子泵菌视紫红质、钠离子泵 KR2、通道视紫红质和鱼腥蓝细菌感受态视紫红质。我们概述了理论生物物理方法在研究视蛋白中的有用性、研究视黄醛活性位点氢键动力学的挑战，以及对膜转运体构象偶联的影响。
