Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models

Area of Science:

• Biophysics
• Molecular Biology
• Computational Chemistry

Background:

• The intracellular environment is a crowded milieu of macromolecules.
• The accuracy of in vitro models, such as polyethylene glycol (PEG) crowders, in mimicking in vivo RNA interactions is not well understood.

Purpose of the Study:

• To investigate the impact of different crowding conditions (dilute, PEG-crowded, and protein-crowded) on the behavior of the HIV-1 TAR RNA hairpin.
• To compare the effects of synthetic PEG crowders versus realistic protein crowders on RNA structure, electrostatics, and dynamics.

Main Methods:

• Utilized all-atom molecular dynamics simulations.
• Analyzed the HIV-1 TAR RNA hairpin in various crowding solutions.

Main Results:

• PEG crowders primarily exert excluded-volume effects, maintaining RNA hydration and ion condensation similar to dilute conditions.
• Protein crowders significantly alter RNA electrostatics, reduce ion condensation by ~60%, displace water, and form specific contacts with charged residues.
• Protein crowding leads to local RNA expansion, altered conformational landscape, and significantly reduced RNA and solvent dynamics, while PEG has minimal effects.

Conclusions:

• The identity of crowders critically influences RNA behavior and interactions within simulated environments.
• Polyethylene glycol (PEG) is not a universal model for intracellular crowding due to its limited representation of complex biological interactions.
• Findings provide mechanistic insights for RNA studies in biologically relevant, crowded conditions.