Increasing the affinity of selective bZIP-binding peptides through surface residue redesign

Area of Science:

• Protein-protein interactions
• Molecular biology
• Drug design

Background:

• Coiled-coil dimers are crucial protein interaction motifs in cellular processes.
• Basic leucine-zipper (bZIP) transcription factors rely on coiled-coil dimerization for function, and their misregulation is linked to diseases like cancer.
• Targeting these coiled-coil interactions with engineered molecules offers therapeutic potential.

Purpose of the Study:

• To investigate the impact of surface residue redesign on the affinity and specificity of engineered anti-bZIP peptides.
• To enhance the binding capabilities of previously designed peptides targeting specific bZIP transcription factors.

Main Methods:

• Design of 'anti-bZIP' peptides focusing on core coiled-coil residues for specificity.
• High-throughput peptide array testing to identify successful binders.
• Solution-based measurement of binding affinities and specificities for selected anti-bZIPs (targeting FOS, XBP1, ATF6, CREBZF).
• Redesign of surface residues to assess effects on binding affinity and specificity.

Main Results:

• Incorporating residues that promote helix formation significantly increased binding affinities for all tested bZIP targets, yielding low-nanomolar binders.
• Redesigning surface residues enhanced binding affinity across all targets.
• Alterations in surface electrostatics sometimes led to changes in the designed peptides' binding specificity.

Conclusions:

• Surface residue engineering, particularly favoring helix formation, is an effective strategy to boost the affinity of coiled-coil targeting peptides.
• The study demonstrates the potential of rationally designed peptides as potent inhibitors of bZIP transcription factor interactions.
• Careful consideration of surface electrostatics is necessary to maintain or optimize binding specificity during peptide redesign.