Crystal structure of an antiviral ankyrin targeting the HIV-1 capsid and molecular modeling of the ankyrin-capsid complex

Abstract

Ankyrins are cellular repeat proteins, which can be genetically modified to randomize amino-acid residues located at defined positions in each repeat unit, and thus create a potential binding surface adaptable to macromolecular ligands. From a phage-display library of artificial ankyrins, we have isolated Ank^GAG1D4, a trimodular ankyrin which binds to the HIV-1 capsid protein N-terminal domain (NTD^CA) and has an antiviral effect at the late steps of the virus life cycle. In this study, the determinants of the Ank^GAG1D4-NTD^CA interaction were analyzed using peptide scanning in competition ELISA, capsid mutagenesis, ankyrin crystallography and molecular modeling. We determined the Ank^GAG1D4 structure at 2.2 Å resolution, and used the crystal structure in molecular docking with a homology model of HIV-1 capsid. Our results indicated that NTD^CA alpha-helices H1 and H7 could mediate the formation of the capsid-Ank ^GAG1D4 binary complex, but the interaction involving H7 was predicted to be more stable than with H1. Arginine-18 (R18) in H1, and R132 and R143 in H7 were found to be the key players of the Ank^GAG1D4-NTD^CA interaction. This was confirmed by R-to-A mutagenesis of NTD^CA, and by sequence analysis of trimodular ankyrins negative for capsid binding. In Ank^GAG1D4, major interactors common to H1 and H7 were found to be S45, Y56, R89, K122 and K123. Collectively, our ankyrin-capsid binding analysis implied a significant degree of flexibility within the NTD^CA domain of the HIV-1 capsid protein, and provided some clues for the design of new antivirals targeting the capsid protein and viral assembly. © 2014 Springer International Publishing.