Download MendeleyComplex water networks visualized by cryogenic electron microscopy of RNA.
Kretsch, R.C., Li, S., Pintilie, G., Palo, M.Z., Case, D.A., Das, R., Zhang, K., Chiu, W.(2025) Nature 642: 250-259
- PubMed: 40068818
- DOI: https://doi.org/10.1038/s41586-025-08855-w
- Primary Citation of Related Structures:
9CBU, 9CBW, 9CBX, 9CBY - PubMed Abstract:
The stability and function of biomolecules are directly influenced by their myriad interactions with water 1-16 . In this study, we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule, the Tetrahymena ribozyme, determined at 2.2 and 2.3 Å resolutions. By employing segmentation-guided water and ion modeling (SWIM) 17,18 , an approach combining resolvability and chemical parameters, we automatically modeled and cross-validated water molecules and Mg 2+ 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.
- Biophysics Program, Stanford University School of Medicine, Stanford, California, USA.
Organizational Affiliation:
