Amide Nitrogen Pyramidalization via N–H/N Interactions that Stabilize the delta/alpha Conformations in Turns, Loops, and 310- and alpha-Helices

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 -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–Hi+1/Ni interaction was obtained. This structure had a close Hi+1•••Ni 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 Ni nitrogen. This pyramidalization reduces the planarity and electron delocalization inherent to an amide bond, as a result of the nitrogen Ni 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 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 indicate that close H•••N distances and substantial Ni 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 delta/alphaR or delta'/alphaL 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 delta/alphaR -> type I beta-turn -> 310-helix -> alpha-helix).