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

TitleIncreasing the affinity of selective bZIP-binding peptides through surface residue redesign.
Publication TypeJournal Article
Year of Publication2014
AuthorsKaplan JB, Reinke AW, Keating AE
JournalProtein Sci
Volume23
Issue7
Pagination940-53
Date Published2014 Jul
ISSN1469-896X
KeywordsBasic-Leucine Zipper Transcription Factors, Drug Design, Humans, Models, Molecular, Peptides, Protein Array Analysis, Protein Binding, Protein Conformation, Protein Structure, Secondary, Static Electricity
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.

DOI10.1002/pro.2477
Alternate JournalProtein Sci.
PubMed ID24729132
PubMed Central IDPMC4088978
Grant ListGM067681 / GM / NIGMS NIH HHS / United States
T32 GM007287 / GM / NIGMS NIH HHS / United States