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

Abstract

The coiled-coil dimer is a prevalent protein interaction motif that is important for many cellular processes. The basic leucine-zipper (bZIP) transcription factors are one family of proteins for which coiled-coil mediated dimerization is essential for function, and misregulation of bZIPs can lead to disease states including cancer. This makes coiled coils attractive protein-protein interaction targets to disrupt using engineered molecules. Previous work designing peptides to compete with native coiled-coil interactions focused primarily on designing the core residues of the interface to achieve affinity and specificity. However, folding studies on the model bZIP GCN4 show that coiled-coil surface residues also contribute to binding affinity. Here we extend a prior study in which peptides were designed to bind tightly and specifically to representative members of each of 20 human bZIP families. These "anti-bZIP" peptides were designed with an emphasis on target-binding specificity, with contributions to design-target specificity and affinity engineered considering only the coiled-coil core residues. High-throughput testing using peptide arrays indicated many successes. We have now measured the binding affinities and specificities of anti-bZIPs that bind to FOS, XBP1, ATF6, and CREBZF in solution and tested whether redesigning the surface residues can increase design-target affinity. Incorporating residues that favor helix formation into the designs increased binding affinities in all cases, providing low-nanomolar binders of each target. However, changes in surface electrostatic interactions sometimes changed the binding specificity of the designed peptides.

• Authors: Jenifer B Kaplan, Aaron W Reinke, Amy E Keating
• Journal: Protein science : a publication of the Protein Society (Protein Sci) Vol. 23 Issue 7 Pg. 940-53 (Jul 2014) ISSN: 1469-896X [Electronic] United States
• PMID: 24729132 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.)
• Copyright: © 2014 The Protein Society.

Chemical References

• Basic-Leucine Zipper Transcription Factors
• Peptides

Topics

• Basic-Leucine Zipper Transcription Factors (antagonists & inhibitors, chemistry, metabolism)
• Drug Design
• Humans
• Models, Molecular
• Peptides (chemistry, metabolism)
• Protein Array Analysis (methods)
• Protein Binding
• Protein Conformation
• Protein Structure, Secondary
• Static Electricity