School of Molecular Sciences and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287-1604, USA.
J Chem Phys. 2019 Mar 7;150(9):094701. doi: 10.1063/1.5081739.
In this molecular dynamics simulation study, we analyze the local structural and dynamic properties of water hydrating the protein ubiquitin on a spatial grid with 1 Å resolution. This allows for insights into the spatial distribution of water number densities, molecular orientations, translations, and rotations as a function of distance from the protein surface. Water molecule orientations follow a heterogeneous distribution with preferred local orientations of water dipoles and O-H bond vectors up to 10-15 Å distances from the protein, while local variations of the water number density converge to homogeneous bulk-like values within less than 8 Å. Interestingly, we find that the long-ranged orientational structure of water does not impact either the translational or rotational dynamics of water. Instead, heterogeneous distributions of local dynamical parameters and averaged dynamical retardation factors are only found close to the protein surface and follow a distance dependence comparable to heterogeneities in the local water number density. This study shows that the formation of nanodomains of preferred water orientations far from the protein does not significantly impact dynamical processes probed as a non-local average in most experiments.
在这项分子动力学模拟研究中，我们分析了在空间网格上以 1Å 分辨率水合蛋白质泛素的局部结构和动态特性。这使我们能够深入了解水分子数密度、分子取向、平移和旋转的空间分布，以及它们与蛋白质表面的距离之间的关系。水分子的取向呈现出不均匀的分布，在距离蛋白质 10-15Å 的范围内，水分子的偶极子和 O-H 键矢量具有优先的局部取向，而水分子数密度的局部变化在不到 8Å 的范围内收敛到均匀的体相值。有趣的是，我们发现水分子的长程取向结构并不影响水分子的平移或旋转动力学。相反，局部动力学参数和平均动力学延迟因子的不均匀分布仅在靠近蛋白质表面时发现，并表现出与局部水分子数密度不均匀性相当的距离依赖性。这项研究表明，在远离蛋白质的地方形成优先取向的纳米域不会显著影响大多数实验中作为非局部平均探测的动力学过程。
