Designed arginine-rich RNA-binding peptides with picomolar affinity

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Arginine-rich peptide motifs (ARMs) are vital for RNA interactions in biological processes.
• Bacteriophage ARMs bind specific RNA hairpin structures, mediating transcription antitermination.
• The P22 bacteriophage antitermination complex exhibits exceptionally strong ARM-RNA binding.

Purpose of the Study:

• To enhance the binding affinity of alpha-helical ARM-RNA interactions.
• To investigate reciprocal design strategies for improving ARM-RNA complex stability.
• To explore novel ARM-RNA interactions beyond native systems.

Main Methods:

• Utilizing a reciprocal design approach to engineer ARM-RNA interactions.
• Characterizing ARM-RNA binding using advanced biophysical techniques.
• Employing mRNA display selection for identifying new ARM-RNA binders.

Main Results:

• Achieved significant enhancement in the binding affinity of two distinct ARM-RNA interactions.
• Demonstrated the efficacy of reciprocal design in strengthening protein-RNA complexes.
• Quantified the dissociation constant of the P22(N21)-P22boxB complex at 200 +/- 56 pM.

Conclusions:

• Reciprocal design is a powerful strategy for optimizing ARM-RNA interactions.
• Enhanced ARM-RNA complexes have potential applications in biotechnology and medicine.
• This work provides new insights into the fundamental mechanisms of RNA recognition by peptides.