Complex Water Networks Visualized through Cryogenic Electron Microscopy of RNA

TL;DR

This paper uses cryo-EM to visualize water networks in RNA, revealing how water mediates RNA interactions and challenges traditional modeling approaches.

Contribution

The study introduces a novel approach to visualize and validate complex water networks in RNA using cryo-EM and molecular dynamics simulations.

Findings

Cryo-EM maps revealed extensive water and Mg2+ involvement in RNA non-canonical interactions.

Unexpectedly similar cryo-EM densities were observed in regions without ordered water modeling.

Cryo-EM densities matched predicted water networks from molecular dynamics simulations.

Abstract

The stability and function of biomolecules are directly influenced by their myriad interactions with water. Nucleic acids are highly solvated and hence uniquely suited for the investigation of water in near-native conditions using cryogenic electron microscopy (cryo-EM). We determined two cryo-EM maps of Tetrahymena ribozyme 2.2 and 2.3 Å resolutions and automatically modeled 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 we do 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. The cryo-EM density can be further compared against various MD simulations enabling evaluation and comparison of the accuracy of various simulation methodologies.