Amide Nitrogen Pyramidalization via N-H/N Interactions that Stabilize the δ/α Conformations in Turns, Loops, and 3₁₀-...

N-H/N interactions, between an amide N-H on one residue (i + 1) and the amide N lone pair on the prior (i) residue, have been observed in key structures in proteins, including turns, loops, and α-helices. However, there remains an incomplete understanding about the inherent nature of N-H/N interactions and how they can impact protein structure and dynamics. The crystal structure of a molecule (Boc-hyp(4-I-Ph)-NHCy) with an N-H_i+1/N_i interaction was obtained. This structure had a close H_i+1···N_i distance of 2.30 Å, well below the 2.75 Å sum of the van der Waals radii of H and N. This structure exhibited substantial (12°; 0.17 Å) pyramidalization (partial sp³ character) of the proline N_i nitrogen. This pyramidalization reduces the planarity and electron delocalization inherent to an amide bond, as a result of the nitrogen N_i lone pair engaging directly with the hydrogen on the subsequent amide. DFT calculations on Ac-Pro-NHMe indicate that nitrogen pyramidalization and partial loss of amide planarity are inherent features of an N-H/N interaction. In addition, calculations demonstrate that the δ conformation, which has an N-H/N interaction, exhibits a substantially lower barrier to proline cis-trans isomerism than the PPII conformation, which lacks an N-H/N interaction, and that a closer N-H/N interaction and greater N pyramidalization are observed in the transition state than in the ground states. Analysis of small-molecule crystal structures indicates that close H···N distances and substantial N_i pyramidalization are inherent to N-H/N interactions. N-H/N interactions are ubiquitous in the PDB at all 20 canonical amino acids when they are in the δ/α_R or δ'/α_L conformations, consistent with N-H/N interactions being central local structural elements in proteins, as well as in early folding transitions in proteins (single residue δ/α_R → type I β-turn → 3₁₀-helix → α-helix).