Complex water networks visualized by cryogenic electron microscopy of RNA

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Biomolecular stability and function are critically dependent on interactions with surrounding water molecules.
• Understanding the role of water in molecular interactions is essential for deciphering biological processes.

Purpose of the Study:

• To investigate the role of water in the structure and function of the highly solvated Tetrahymena ribozyme using cryo-electron microscopy (cryo-EM).
• To develop and apply an automated method for modelling water and ions in complex biomolecular systems.

Main Methods:

• Utilized cryogenic electron microscopy (cryo-EM) to obtain high-resolution structural data of the Tetrahymena ribozyme.
• Employed segmentation-guided water and ion modelling (SWIM) to automatically model water molecules and Mg2+ ions.
• Integrated cryo-EM density analysis with molecular dynamics simulations to interpret unmodelled densities.

Main Results:

• Successfully modelled extensive water networks and Mg2+ ions within the ribozyme core, highlighting water's role in mediating non-canonical RNA interactions.
• Identified unmodelled, yet consistent, densities in cryo-EM maps corresponding to complex water networks, as predicted by molecular dynamics.
• Provided a biophysical explanation for the elusiveness of certain water networks to conventional atomic modelling.

Conclusions:

• Demonstrated a novel approach to visualize and characterize both ordered and flexible water molecules interacting with biomolecules using cryo-EM and computational methods.
• The study underscores the significant, often overlooked, contribution of water networks to biomolecular structure and function.
• Advanced the understanding of hydration dynamics in RNA molecules and provided a framework for studying other solvated biomolecular systems.