Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains

Area of Science:

• Molecular Biology
• Biophysics
• Genomics

Background:

• Cellular functions depend on high-affinity RNA-protein interactions.
• Individual RNA-binding domains often show limited specificity and affinity compared to DNA-binding domains.
• Current methods like RNA SELEX show limited enrichment for optimal binding motifs.

Purpose of the Study:

• To investigate how cooperative binding of multiple domains in RNA-binding proteins (RBPs) enhances effective affinity and specificity.
• To develop a thermodynamic model predicting the binding avidity of multi-domain RBPs.
• To rationalize the role of clustered binding motifs in RBP function.

Main Methods:

• Development of a thermodynamic model for calculating effective binding affinity (avidity).
• Model applied to idealized, sequence-specific RBPs with varying numbers of RNA-binding domains (RBDs).
• Comparison of model predictions with experimental measurements for seven known proteins.

Main Results:

• Model predictions showed good agreement with experimental measurements for seven proteins.
• Demonstrated that cooperative binding can increase effective affinity and specificity by orders of magnitude.
• Showed that a two-fold difference in binding site density can lead to a ten-fold increase in protein occupancy.

Conclusions:

• Multi-domain architecture is crucial for achieving high-affinity and specific RNA binding.
• Local clusters of binding motifs are likely the physiological targets for multi-domain RBPs.
• The developed thermodynamic model provides a quantitative framework for understanding RBP-RNA interactions.