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

Area of Science:

• Bacterial regulatory networks
• RNA-protein interactions
• Molecular mechanisms of gene regulation

Background:

• The Csr/Rsm system controls bacterial gene expression via non-coding RNAs (ncRNAs) and regulatory proteins.
• In Pseudomonas protegens, RsmZ ncRNA sequesters RsmE protein dimers, acting as a 'protein sponge' to regulate translation.
• The binding of RsmE to RsmZ exhibits negative cooperativity, where initial binding reduces affinity for subsequent binding events.

Purpose of the Study:

• To elucidate the molecular mechanism behind the negative cooperativity observed in RsmE binding to RsmZ.
• To understand how this mechanism facilitates the handover of RsmE from mRNA to ncRNA.

Main Methods:

• Isothermal Titration Calorimetry (ITC) to measure binding thermodynamics.
• Nuclear Magnetic Resonance (NMR) spectroscopy to probe structural and dynamic changes.
• Molecular Dynamics (MD) simulations to model the allosteric mechanism.

Main Results:

• An allosteric mechanism, analogous to a Newton's cradle, was identified.
• Binding at one site on RsmZ induces conformational and dynamic changes at a second site.
• This allosteric coupling explains the reduced affinity for the second RsmE dimer binding and facilitates protein handover.

Conclusions:

• The Newton's cradle-like allosteric mechanism governs RsmE binding to RsmZ in Pseudomonas protegens.
• This mechanism is crucial for the efficient handover of RsmE dimers from target mRNAs to the RsmZ ncRNA.
• Understanding this process provides insights into bacterial gene regulation and RNA-protein interactions.