Newton's cradle-like allosteric mechanism explains regulatory RsmE RNA binding

Area of Science:

• Bacterial gene regulation
• RNA-protein interactions
• Molecular mechanisms

Background:

• The Csr/Rsm system controls mRNA translation in bacteria via non-coding RNAs (ncRNAs) and regulatory proteins.
• In Pseudomonas protegens, RsmZ ncRNA acts as a 'protein sponge', sequestering RsmE protein dimers to regulate translation.
• RsmZ exhibits unusual negative cooperativity in RsmE binding, where initial binding reduces affinity at subsequent sites.

Purpose of the Study:

• To elucidate the molecular mechanisms underlying the negative cooperativity in RsmE binding to RsmZ ncRNA.
• To understand how this negative cooperativity facilitates the release of RsmE from mRNA.

Main Methods:

• Isothermal Titration Calorimetry (ITC) to measure binding thermodynamics.
• Nuclear Magnetic Resonance (NMR) spectroscopy to probe structural changes.
• Molecular Dynamics (MD) simulations to model protein-RNA interactions and conformational dynamics.

Main Results:

• The initial RsmE binding event to RsmZ increases conformational entropy at the unoccupied binding site, leading to partial unfolding of the C-terminal helix.
• An allosteric mechanism couples RNA binding at one site to conformational changes at another, explaining the reduced affinity for subsequent binding.
• Anti-parallel β-sheets within the RsmE dimer mediate inter-site communication, involving H-bond constriction and relaxation.

Conclusions:

• Negative cooperativity in RsmZ-RsmE interaction is driven by allosteric conformational changes and entropy.
• This mechanism allows efficient handover of RsmE from mRNA to ncRNA, fine-tuning bacterial gene expression.
• The findings reveal a novel mode of allosteric regulation in RNA-protein interactions.