Kretsch Rachael C, Li Shanshan, Pintilie Grigore, Palo Michael Z, Case David A, Das Rhiju, Zhang Kaiming, Chiu Wah
Biophysics Program, Stanford University School of Medicine, CA USA.
Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.
bioRxiv. 2025 Jan 24:2025.01.23.634578. doi: 10.1101/2025.01.23.634578.
The stability and function of biomolecules are directly influenced by their myriad interactions with water. In this study, we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule, the ribozyme, determined at 2.2 and 2.3 Å resolutions. By employing segmentation-guided water and ion modeling (SWIM), an approach combining resolvability and chemical parameters, we automatically modeled and cross-validated water molecules and Mg ions in the ribozyme core, revealing the extensive involvement of water in mediating RNA non-canonical interactions. Unexpectedly, in regions where SWIM does not model ordered water, we observed highly similar densities in both cryo-EM maps. In many of these regions, the cryo-EM densities superimpose with complex water networks predicted by molecular dynamics (MD), supporting their assignment as water and suggesting a biophysical explanation for their elusiveness to conventional atomic coordinate modeling. Our study demonstrates an approach to unveil both rigid and flexible waters that surround biomolecules through cryo-EM map densities, statistical and chemical metrics, and MD simulations.
生物分子的稳定性和功能直接受到它们与水的无数相互作用的影响。在本研究中，我们通过低温电子显微镜（cryo-EM）对一种高度水合的分子——核酶进行了研究，该研究在2.2 Å和2.3 Å分辨率下完成。通过采用分割引导的水和离子建模（SWIM），一种结合可分辨性和化学参数的方法，我们自动对核酶核心中的水分子和镁离子进行了建模和交叉验证，揭示了水在介导RNA非规范相互作用中的广泛参与。出乎意料的是，在SWIM未对有序水进行建模的区域，我们在两个低温电子显微镜图谱中都观察到了高度相似的密度。在许多这些区域，低温电子显微镜密度与分子动力学（MD）预测的复杂水网络重叠，支持将它们归为水，并为它们难以用传统原子坐标建模提供了生物物理解释。我们的研究展示了一种通过低温电子显微镜图谱密度、统计和化学指标以及分子动力学模拟来揭示围绕生物分子的刚性和柔性水的方法。
