Complex water networks visualized by cryogenic electron microscopy of RNA

• 成果类型: Article
• 署名作者: Kretsch, Rachael C.; Li, Shanshan; Pintilie, Grigore; Palo, Michael Z.; Case, David A.; Das, Rhiju; Zhang, Kaiming; Chiu, Wah
• 署名单位: Stanford University; Chinese Academy of Sciences; University of Science & Technology of China, CAS; Stanford University; Stanford University; Stanford University; Rutgers University System; Rutgers University New Brunswick; Stanford University; Stanford University; Howard Hughes Medical Institute; Stanford University; Stanford University; United States Department of Energy (DOE); SLAC National Accelerator Laboratory
• 刊物名称: Nature
• ISSN/ISSBN: 0028-2659
• DOI: 10.1038/s41586-025-08855-w
• 发表日期: 2025-06-05
• 关键词: molecular-dynamics simulations; cryo-em; structural basis; ribozyme domain; force-field; hydration; ion; validation; solvation; solvent

摘要

The stability and function of biomolecules are directly influenced by their myriad interactions with water1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15-16. Here we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule: the Tetrahymena ribozyme. By using segmentation-guided water and ion modelling (SWIM)17,18, an approach combining resolvability and chemical parameters, we automatically modelled and cross-validated water molecules and Mg2+ 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, supporting their assignment as water and suggesting a biophysical explanation for their elusiveness to conventional atomic coordinate modelling. 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 molecular dynamics simulations.