Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 17, 1090 Vienna, Austria.
Phys Chem Chem Phys. 2019 Feb 20;21(8):4435-4443. doi: 10.1039/c8cp07623e.
The time-dependent Stokes shift (TDSS) has attracted increasing interest for measuring hydration dynamics around biomolecules during the last decades. Its ability to report on hydration dynamics around proteins, however, was questioned recently since the experimental signal stems from both water and protein motion with an unknown ratio of contribution. Using large-scale computer simulations, we examine the ability of the TDSS to capture local hydration dynamics at nine different sites around the protein ubiquitin. By computationally constraining protein motion, it is shown that the remaining water component is meaningful and in line with the picture of a heterogeneous yet overall mobile hydration layer. However, protein contributions are excessively large and cannot be removed in an experimental context, thus obscuring the water component. Consequently, we conclude that the experimental TDSS may not be suitable for the investigation of hydration dynamics around proteins.
在过去几十年中，时间相关的斯托克斯位移（TDSS）因其能够测量生物分子周围水合动力学而引起了越来越多的关注。然而，最近有人质疑它在测量蛋白质周围水合动力学方面的能力，因为实验信号源自水和蛋白质运动，其贡献比例未知。本研究使用大规模计算机模拟，考察了 TDSS 在蛋白质泛素九个不同位置捕捉局部水合动力学的能力。通过计算限制蛋白质运动，结果表明，剩余的水成分是有意义的，与异质但整体可移动水合层的图像一致。然而，蛋白质的贡献过大，在实验环境中无法去除，从而掩盖了水的成分。因此，我们得出结论，实验 TDSS 可能不适合研究蛋白质周围的水合动力学。
