Nature of Amide Carbonyl-Carbonyl Interactions in Proteins

Noncovalent interactions define and modulate biomolecular structure, function, and dynamics. In many protein secondary structures, an intimate interaction exists between adjacent carbonyl groups of the main-chain amide bonds. As this short contact contributes to the energetics of protein conformational, stability as welt as protein-ligand interactions, understanding its nature is crucial. The intimacy of the carbonyl groups could arise from a charge-charge or dipole-dipole interaction, or n ->pi* electronic delocalization. This last putative origin, which is reminiscent of the Burgi-Dunitz trajectory, involves delocalization of the lone pairs (n) of the oxygen (Oi-1,) of a peptide bond over the antibonding orbital, (pi*) of the carbonyl group (C-r=O-i) of the subsequent peptide bond. By installing isosteric chemical substituents in a peptidic model system and using NMR spectroscopy, X-ray diffraction analysis, and ab initio calculations to analyze the consequences, the intimate interaction between adjacent carbonyl groups is shown to arise primarily from n ->pi* electronic delocalization. This finding has implications for organic, biological, and medicinal chemistry.