Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution

• Published in: Angewandte Chemie International Edition 2014-01, Vol.53 (3), p.883-887
• Main Authors: Buratto, Jérémie, Colombo, Cinzia, Stupfel, Marine, Dawson, Simon J., Dolain, Christel, Langlois d'Estaintot, Béatrice, Fischer, Lucile, Granier, Thierry, Laguerre, Michel, Gallois, Bernard, Huc, Ivan
• Format: Article
• Language: English
• Subjects: Amides - chemistry; Amides - metabolism; Binding Sites; Carbonic Anhydrase II - chemistry; Carbonic Anhydrase II - metabolism; Carbonic Anhydrase Inhibitors - chemistry; Carbonic Anhydrase Inhibitors - metabolism; Circular Dichroism; crystallography; Crystallography, X-Ray; foldamers; Humans; Molecular Dynamics Simulation; Protein Binding; protein recognition; Protein Structure, Secondary; Protein Structure, Tertiary; solid-phase synthesis; Surface Plasmon Resonance
• ISSN: 1433-7851; 1521-3773
• DOI: 10.1002/anie.201309160

In the search of molecules that could recognize sizeable areas of protein surfaces, a series of ten helical aromatic oligoamide foldamers was synthesized on solid phase. The foldamers comprise three to five monomers carrying various proteinogenic side chains, and exist as racemic mixtures of interconverting right‐handed and left‐handed helices. Functionalization of the foldamers by a nanomolar ligand of human carbonic anhydrase II (HCA) ensured that they would be held in close proximity to the protein surface. Foldamer–protein interactions were screened by circular dichroism (CD). One foldamer displayed intense CD bands indicating that a preferred helix handedness is induced upon interacting with the protein surface. The crystal structure of the complex between this foldamer and HCA could be resolved at 2.1 Å resolution and revealed a number of unanticipated protein–foldamer, foldamer–foldamer, and protein–protein interactions. To design a foldamer that binds to a protein surface, a strategy is proposed that uses a known protein ligand to tether the foldamer to the protein surface. Candidates are first screened for induced circular dichroism in presence of the protein. Then, structural information about foldamer–protein interactions is collected before strong binding is established. The crystal structure of human carbonic anhydrase (A, B chains) with helical aromatic amide foldamers (stick models) is shown.